Delta Users Guide

Delta NMR Software Users Guide
Copyright 1990-2000 by JEOL USA, INC. Eleven Dearborn Road Peabody, MA 01960-3823 All Rights Reserved
DELTA Users Guide, v 3.2
Trademarks
GLTM, Indigo, Indigo MagicTM, Indigo2TM,IRIX, OpenGL, SGITM, Silicon Graphics Octane, and Silicon Graphics are trademarks of Silicon Graphics, Inc. UNIX is a trademark registered in the United States and other countries, licensed exclusively through X/Open Company, Ltd. X Window System is a trademark of Massachusetts Institute of Technology. Motif is a trademark of Open Software Foundation, Inc. PostScript is a trademark of Adobe Systems Incorporated All other company and product names are trademarks or registered trademarks of their respective companies.
Table of Contents
Table of Contents................................................................................................................. i List of Figures .................................................................................................................... ix List of Tables ................................................................................................................... xiii Chapter 1. Introduction................................................................................................... 1-1 Introduction................................................................................................................ 1-1 About This Guide....................................................................................................... 1-1 Before You Begin ...................................................................................................... 1-1 Special Symbols......................................................................................................... 1-1 Font Conventions ....................................................................................................... 1-1 Keystroke Conventions.............................................................................................. 1-2 Color Conventions ..................................................................................................... 1-2 Chapter 2. User Interface Basics .................................................................................... 2-1 Power-on .................................................................................................................... 2-1 Login .......................................................................................................................... 2-1 Mouse and Keyboard ................................................................................................. 2-3 Input Focus........................................................................................................... 2-3 Keyboard.............................................................................................................. 2-3 Structure of a Window ......................................................................................... 2-3 Window Menu Buttons .............................................................................................. 2-4 Iconifying or Minimizing Windows....................................................................... 2-5 Maximizing Windows to Full Screen ........................................................................ 2-6 Moving Windows....................................................................................................... 2-6 Resizing Windows ..................................................................................................... 2-6 Toolchest.................................................................................................................... 2-6 Workstation System Usage ........................................................................................ 2-8 Terminal Shell............................................................................................................ 2-8 Logout Window ......................................................................................................... 2-9 Chapter 3. Getting Started On Delta .............................................................................. 3-1 Introduction................................................................................................................ 3-1 Starting DELTA......................................................................................................... 3-1 The Delta Console...................................................................................................... 3-2 The Delta Console Menu Bar .................................................................................... 3-3 Pull-Down Menus ................................................................................................ 3-3 Accelerator Keys.................................................................................................. 3-3 Tool Bar Icons............................................................................................................ 3-3 Exiting Delta .............................................................................................................. 3-6 On-line Help .............................................................................................................. 3-6 Preferences Tool ........................................................................................................ 3-7 File Manager ............................................................................................................ 3-15 File Converter .......................................................................................................... 3-17 Chapter 4. Eclipse Spectrometer Control ....................................................................... 4-1
Introduction................................................................................................................ 4-1 Spectrometer to Host Workstation Communication .................................................. 4-1 Spectrometer Control Tool ........................................................................................ 4-2 Selecting a Spectrometer............................................................................................ 4-2 Default Spectrometer Connection........................................................................ 4-5 Spectrometer Control Tools....................................................................................... 4-7 Spectrometer Control Tools...................................................................................... 4-9 Sample Control Tool.................................................................................................. 4-9 Shim Tool Controls............................................................................................ 4-13 Queue Management ................................................................................................. 4-21 Experiment Data ................................................................................................ 4-22 Additional Experiment Information................................................................... 4-23 Deleting Queue items........................................................................................ 4-23 Experiment Tool ...................................................................................................... 4-24 Experiment Selection ........................................................................................ 4-25 Local Experiment Directory .............................................................................. 4-25 Global Experiment Directory............................................................................. 4-25 Loading an Experiment...................................................................................... 4-26 The Header Section............................................................................................ 4-26 The Instrument Section ...................................................................................... 4-29 The Acquisition Section..................................................................................... 4-30 The Pulse Section............................................................................................... 4-31 Automation Window................................................................................................ 4-34 Automation Queue ............................................................................................. 4-37 Automation Console ................................................................................................ 4-38 Automation Editor ................................................................................................... 4-39 Methods for Customizing Automation .............................................................. 4-41 Lock Signal Display - Sawtooth .............................................................................. 4-43 View Tool ................................................................................................................ 4-44 Copy......................................................................................................................... 4-46 Chapter 5. Processing 1D Data....................................................................................... 5-1 Introduction................................................................................................................ 5-1 1D Processor .............................................................................................................. 5-2 Default Start-up Mode ......................................................................................... 5-3 1D Processor Start-Up Procedure .............................................................................. 5-4 The Open File Tool.............................................................................................. 5-4 1D Processor Window - Extended Mode................................................................... 5-6 Processing Lists ................................................................................................... 5-7 Extended Mode Icon Buttons - Top Row .......................................................... 5-10 Extended Mode 1D Processing Icons -- Second Row ....................................... 5-13 Menus for Extended 1D Processing......................................................................... 5-14 PreTransform Functions..................................................................................... 5-14 Window Functions ............................................................................................. 5-17 Transform Functions.......................................................................................... 5-17 Cursor Tool .............................................................................................................. 5-19 Cursor Modes........................................................................................................... 5-22
Zoom, Region, PiP -- a Sampler ........................................................................ 5-23 Menus for Extended 1D Processing........................................................................ 5-26 Post Transform Functions .................................................................................. 5-26 Display Functions .............................................................................................. 5-33 Integrals.............................................................................................................. 5-46 Peak Deconvolution ........................................................................................... 5-51 Annotation.......................................................................................................... 5-55 Molecules........................................................................................................... 5-57 Data Window Manipulations: Level Tool ............................................................... 5-59 Data Window Manipulations: Geometry Options Menu ......................................... 5-60 Data Information Display: Spreadsheet Tool .......................................................... 5-64 Loading Data into the Spread Sheet................................................................... 5-65 Drag and Drop.................................................................................................... 5-65 Saving Processed Data............................................................................................. 5-66 Plotting Data ............................................................................................................ 5-67 Presentation Manager............................................................................................... 5-69 Presentation Manager Templates....................................................................... 5-70 Presentation Manager Boxes.............................................................................. 5-72 Ruler Links Tool ................................................................................................ 5-72 Presentation Manager Menus................................................................................... 5-77 Presentation Manager Tool Bar ............................................................................... 5-77 Simple Mode 1D Processing.................................................................................... 5-78 Simple Mode Processor Buttons........................................................................ 5-79 Chapter 6. Using Data Slate ........................................................................................... 6-1 Loading Data into the Data Slate ............................................................................... 6-2 Data Source Toggle Buttons ................................................................................ 6-2 Loading Multiple Data Files ...................................................................................... 6-3 Horizontal and Vertical Views............................................................................. 6-3 Box Data View..................................................................................................... 6-4 Selecting Active Data Sets......................................................................................... 6-5 Data Slate Icons ......................................................................................................... 6-7 The File Math Tool ............................................................................................ 6-10 Connected Objects ................................................................................................... 6-11 Individual Data Presentation Control................................................................. 6-12 Panning, Rotating and Expanding Data ............................................................. 6-13 Peak Picking, Data Reduction and Integration ........................................................ 6-14 Peak Deconvolution ........................................................................................... 6-14 Annotation................................................................................................................ 6-14 Spreadsheet Tool...................................................................................................... 6-14 Plotting Data ............................................................................................................ 6-14 Connect Options on the View Menu........................................................................ 6-15 Advanced Data Slate Operations ............................................................................. 6-15 Slicing ................................................................................................................ 6-15 Expansion........................................................................................................... 6-17 Chapter 7. Processing 2D Data....................................................................................... 7-1
Introduction................................................................................................................ 7-1 Loading 2D Data into the nD Processor .................................................................... 7-1 Elements of 2D Processing ........................................................................................ 7-3 Preparing 2D Processing Lists ................................................................................... 7-5 Selecting a Data Output destination..................................................................... 7-8 Toggling between processing list view and geometry view: ............................... 7-9 Selecting Preferences ........................................................................................... 7-9 Loading and Processing 1D Slices............................................................................. 7-9 Phasing 2D Data ...................................................................................................... 7-10 2D Phasing Tool ................................................................................................ 7-10 2D Viewer Tool ....................................................................................................... 7-13 Two Dimensional Display Modes ..................................................................... 7-14 2D Cursor Tool functions .................................................................................. 7-17 Contouring 2D Data........................................................................................... 7-17 Overview Area ................................................................................................... 7-21 Zooming and Panning 2D Data.......................................................................... 7-21 Slice and Projection Areas ................................................................................. 7-22 2D Peak Pick and Data Reduction ........................................................................... 7-23 Peak Grouping ................................................................................................... 7-25 Peak Melding ..................................................................................................... 7-26 Integrating 2D Data............................................................................................ 7-27 Annotating 2D Spectra....................................................................................... 7-27 Spreadsheet Tool................................................................................................ 7-30 Plotting 2D Data ............................................................................................... 7-30 Chapter 8. Processing Relaxation Data .......................................................................... 8-1 Introduction................................................................................................................ 8-1 Collecting Relaxation Data ........................................................................................ 8-1 Collecting T1 Data..................................................................................................... 8-3 Calculating Relaxation Times.................................................................................... 8-3 Chapter 9. Processing 3D Data....................................................................................... 9-1 Introduction................................................................................................................ 9-1 Loading 3D Data into the nD Processor .................................................................... 9-1 Elements of 3D Processing ........................................................................................ 9-2 Domains ............................................................................................................... 9-2 Processing Lists ................................................................................................... 9-3 Creating a Processing List ................................................................................... 9-5 Building and Manipulating Processing Lists ....................................................... 9-6 Editing a Processing List ..................................................................................... 9-6 Loading and Processing 1D Slices....................................................................... 9-7 3D Data Slate ............................................................................................................. 9-8 3D Viewer.................................................................................................................. 9-8 Three-Dimensional Display Modes ................................................................... 9-10 Loading 3D Data................................................................................................ 9-12 3D Slicer .................................................................................................................. 9-12 Multidimensional geometry options .................................................................. 9-13
3D Slice Plotter ........................................................................................................ 9-13 Cursor Tool ........................................................................................................ 9-15 Rotating and Translating 3D Data ..................................................................... 9-18 Slice and Projection Areas ................................................................................. 9-18 3D Peak Pick and Data Reduction ..................................................................... 9-18 Chapter 10. Experiment Tool and Eclipse Experiment Programming......................... 10-1 Introduction.............................................................................................................. 10-1 Definition ................................................................................................................. 10-1 Pulse Sequences ................................................................................................. 10-2 Parameter Files................................................................................................... 10-2 Loading Experiments ............................................................................................... 10-2 Spectrometer Control Tool ................................................................................ 10-2 Experiment Tool ...................................................................................................... 10-5 Loading Experiments from Other Data Sets...................................................... 10-5 Syntax and Operators............................................................................................... 10-7 Syntax Rules ...................................................................................................... 10-7 Operators............................................................................................................ 10-8 Define statement .............................................................................................. 10-13 Strings .............................................................................................................. 10-13 Units................................................................................................................. 10-14 Align ................................................................................................................ 10-14 Macro ............................................................................................................... 10-14 Loop ................................................................................................................. 10-15 Begin ................................................................................................................ 10-15 Conditional if-then-else statements.................................................................. 10-15 Include files............................................................................................................ 10-16 User Include Files ............................................................................................ 10-16 Standard Include Files...................................................................................... 10-16 Standard Include Files..................................................................................... 10-16 Header Section ....................................................................................................... 10-17 filename............................................................................................................ 10-17 sample_id ......................................................................................................... 10-18 comment........................................................................................................... 10-18 process.............................................................................................................. 10-18 Autosample Changer slot................................................................................. 10-19 Header Flags .................................................................................................... 10-19 Header Parameters ........................................................................................... 10-22 Adding Header Flags and Parameters Dynamically ........................................ 10-23 Instrument Section ................................................................................................. 10-23 Solvent ............................................................................................................. 10-24 Receiver gain (recvr_gain)............................................................................... 10-24 Temperature control (temp_state and temp_set).............................................. 10-25 Adding Instrument Parameters Dynamically................................................... 10-26 Acquisition Section................................................................................................ 10-26 Domains ........................................................................................................... 10-27 Spectral Offset ................................................................................................. 10-27
Spectral (Sweep) Widths.................................................................................. 10-28 Data Points ....................................................................................................... 10-28 Scans ................................................................................................................ 10-28 Prescans............................................................................................................ 10-29 Pulse Section.......................................................................................................... 10-29 total_time ......................................................................................................... 10-30 x_pulse ............................................................................................................. 10-30 relaxation_delay.............................................................................................. 10-30 j_constant ......................................................................................................... 10-30 Submitting Experiments ........................................................................................ 10-32 Probe Codes and Probe Files ........................................................................... 10-32 Probe Attributes ............................................................................................... 10-33 90 Degree Pulses.............................................................................................. 10-33 Spin Lock Pulses.............................................................................................. 10-34 Temperature Limits.......................................................................................... 10-34 Irr_code ............................................................................................................ 10-34 Domains ........................................................................................................... 10-35 Probe Tuning Values........................................................................................ 10-35 Calculations............................................................................................................ 10-36 Calculation of Pulse Widths and Angles ......................................................... 10-36 Calculation of Audio Filter Delays .................................................................. 10-37 Total Time........................................................................................................ 10-38 Phase Tables........................................................................................................... 10-38 Concatenation of Phase Sets ............................................................................ 10-39 Addition of Phase Sets ..................................................................................... 10-39 90 Degree Phases ............................................................................................. 10-40 Sub-90 Degree Phases...................................................................................... 10-40 Multiple Buffer Acquisition................................................................................... 10-40 module_config Options.......................................................................................... 10-41 Hardware Options ............................................................................................ 10-41 Collection Mode..................................................................................................... 10-43 Macros.................................................................................................................... 10-43 Pulse Programs....................................................................................................... 10-44 Specifications................................................................................................... 10-44 Begin/end Statement ........................................................................................ 10-44 Time States....................................................................................................... 10-44 Referencing Time Variables ............................................................................ 10-44 Referencing Spectrometer Parameters............................................................. 10-44 In-line Calculations.......................................................................................... 10-45 End of Sequence .............................................................................................. 10-45 Gate Assignments and Options.............................................................................. 10-45 RF Gates........................................................................................................... 10-46 RF Phase .......................................................................................................... 10-46 Attenuators....................................................................................................... 10-46 Frequency Offset.............................................................................................. 10-46 Noise Modulation............................................................................................. 10-46
Acquisition Macro ........................................................................................... 10-47 Interactions with irr_code and module_config ................................................ 10-47 Compiling and Error Messages.............................................................................. 10-48 Arrayed Parameters................................................................................................ 10-48 Interaction with multi_file Option ................................................................... 10-48 Syntax .............................................................................................................. 10-49 Exceptions to Arrayed Parameters......................................................................... 10-50 Setting Array Parameters ....................................................................................... 10-50 Collecting T1 Data................................................................................................. 10-51 Appendix A. Standard Include Files A-1 std_acquisition .......................................................................................................... A-1 std_2d_acquisition .................................................................................................... A-1 std_3d_acquisition .................................................................................................... A-2 set_dec_instrument ................................................................................................... A-2 std_domains .............................................................................................................. A-3 std_domaind_master_list .......................................................................................... A-3 std_header ................................................................................................................. A-4 std_instrument........................................................................................................... A-5 std_pulse ................................................................................................................... A-5 std_solid_instrument ................................................................................................. A-6 Appendix B. Instrument Parameters B-1 Appendix C. Irradiation Codes C-1 Appendix D. Decoupling on a GX, GSX, or CPF Delta Upgrade Spectrometer D-1 Proton decoupling from either IRR or TRR channel ................................................ D-1 High Power 1H Decoupler Sequences from either IRR or TRR channel................. D-2 Bilevel 1H Decoupling ............................................................................................. D-2 Low frequency (X-nucleus) decoupling from the TRR channel .............................. D-2 Appendix E. Directories and Files used by Delta E-1 Delta User Account....................................................................................................E-1 Delta System Directories, /usr/delta/ .........................................................................E-3 /usr/delta/global/ Files................................................................................................E-3 /usr/delta/global/ Directories....................................................................................E-13 /usr/delta/setup/ ........................................................................................................E-14 Eclipse Files for Acquisition system........................................................................E-16 Delta Configuration Files.........................................................................................E-17 Eclipse Spectrometer Files and Directories .............................................................E-46 Machine action files.................................................................................................E-59 /eclipse/shapes/ ..................................................................................................E-63 /eclipse/ Program Files.......................................................................................E-64 /usr/eclipse/testprogs/.........................................................................................E-67 /etc/init.d ............................................................................................................E-68 Appendix F. Description of the Automation Template File F-1 SAMPLES ................................................................................................................. F-1 METHODS ................................................................................................................ F-2
GROUPS.................................................................................................................... F-3 EXPERIMENTS and PRESENTATIONS ................................................................ F-4 Experiments ......................................................................................................... F-4 Presentations ........................................................................................................ F-7 Logic of Flow in the Automation Editor.................................................................... F-9 Appendix G. Presentation Manager and Template File Format G-1 Console commands ................................................................................................... G-1 A sample template File (.pmt) ............................................................................ G-2 Appendix H. Terminal Console Program H-1 Appendix I. Tool Icons I-1 Appendix J. Unix and Vi Commands J-1 I. Unix Commands ......................................................................................................J-1 II. VI Commands ........................................................................................................J-2 Appendix K. Installing JEOL AutoTune probes K-1 Probe Tuning............................................................................................................. K-3 Appendix L. Delta V3.2 Software Installation and Configuration Instructions L-1 I. System Requirements for Delta V3.2 .....................................................................L-1 Workstations: .......................................................................................................L-1 SGI - IRIX: .........................................................................................................L-1 Intel - Linux .........................................................................................................L-1 IBM - AIX............................................................................................................L-2 Sun - Solaris.........................................................................................................L-2 Acquisition Systems: ...........................................................................................L-2 NMR Spectrometers: ...........................................................................................L-2 II. Preparing for the Delta V3.2 Software Installation or Upgrade............................L-2 III. Installing or Upgrading the Delta Software on SGI IRIX Systems ..................L-3 IV. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System from an SGI Workstation ........................................................................................................L-5 V. Installing or Upgrading the Delta Software on Intel Linux or Sun Solaris Systems .. L-6 VI. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System from Linux, or Solaris.........................................................................................................L-7 VII. Installing or Upgrading the Delta Software on IBM AIX Systems ...................L-7 VIII. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System from AIX. ...........................................................................................................................L-8 IX. USER Account Setup ..........................................................................................L-8 Appendix M. X Windows Emulation M-1 SGI IRIX setup: ..................................................................................................M-1 X-Server Requirements for PC or MAC:............................................................M-1 PC X-Servers: .....................................................................................................M-2 MAC X-Servers: .................................................................................................M-2 Index ..................................................................................................................................I-i
List of Figures
Silicon Graphics Login Screen 2-1 Silicon Graphics User Interface Screen (detail) 2-2 Basic IRIX Window Structure 2-4 Window Menu Button 2-5 Minimized and Maximized Windows 2-5 Moving and Resizing Windows 2-6 Silicon Graphics User Toolchest 2-7 Selected Menu 2-7 System Usage Monitor 2-8 Silicon Graphics UNIX Shell Window 2-9 Silicon Graphics Logout Confirmation Window 2-9 The Delta Console Window 3-2 Delta Console Menu Bar 3-3 Delta Console Tool Bar 3-4 Confirm window 3-6 Preferences Tool - Personal Page 3-7 Search Tool 3-10 Directory Tool 3-11 Preferences Tool - Data Page 3-12 Preferences Tool - Geometry Page 3-13 Preferences Tool - Miscellaneous Page 3-14 File Manager 3-15 Data File Converter 3-17 Delta Console Window 4-2 Spectrometer Control Tool 4-3 Spectrometer Control Tool Top Buttons 4-3 Spectrometer Control Tool Info Display 4-4 Spectrometer Control window after connection of the workstation and spectrometer 4-5 Spectrometer Control Tool in Monitor Mode 4-6 Spectrometer Control Tool Lower Buttons 4-7 Sample/Shim Tool 4-9 Lock Control section displays the NMR-lock level 4-13 Set the axis for shimming 4-13 System Shims Acknowledge Window 4-15 Open Shim File window 4-16 Save Shim File window 4-17 Lock Level Meter (Minimum 0, Maximum 4095) 4-18 Lock Control 4-18 Gradient Shim and Lock Buttons 4-18 Acknowledge message window 4-22 Spectrometer Control with Experiment Pending 4-22 Spectrometer Control with Experiment Running 4-22 Experiment Information Window 4-23
ix
Open Experiment Tool 4-25 Experiment Header Section 4-27 Set Process Window 4-28 Experiment Instrument Section 4-30 Experiment Acquisition Section 4-31 Experiment Pulse Section 4-32 Pulse Viewer 4-33 Automation Tool 4-34 Automation Queue Window 4-37 Automation Console 4-38 Automation Editor 4-39 Flow Chart for an Automation Editor 4-42 SAWTH or swept lock signal display 4-44 View Tool -- raw data 4-45 View Tool - processed data 4-46 1D Processor 5-1 1D Processor with untransformed and processed data 5-2 Open File Tool Window 5-4 Extended Mode 1D Processor after Performing FFT and Phasing 5-6 1D Processing List 5-7 Open Process List window 5-8 Save Data File window 5-12 Empty Process List 5-16 Process List after Adding DC balance 5-16 Process List after Adding DC Balance and Zerofilling 5-16 Process list after adding Window function 5-17 Process list after adding Fast Fourier Transform 5-18 1D Zoom mode operations 5-19 Sample Key command menu 5-21 Sample Zoom Operation 5-23 Sample Region Operation 5-24 Sample PiP Operation 5-25 Spectrum before Phase Correction. 5-27 Phase Correction Performed Using P0 5-28 Further Phase Correction Using P1 5-28 Applying the Phase Correction 5-29 Interactive Baseline Correction - a) Polynomial and b) Piece wise Linear 5-31 Interactive Baseline Correction Preview 5-32 Interactive Baseline Correction with Show Curve Enabled 5-32 Process list after converting data axis to PPM 5-34 Reference Tool 5-34 Reference in Processing List 5-35 Copy Reference Tool 5-36 Spreadsheet Tool 5-38 1D Processor with auto-peakpicked 1H data 5-40 1D Processor with adjusted peak threshold 5-41
Pick Tool 5-42 Peak Pick Threshold Display 5-43 Peak Display (default) 5-45 Peak Display with Peaks Above Option Enabled 5-46 Peak Display with J Coupling Constants 5-46 1D processor with data peaks integrated 5-47 Integral Slope Adjustment 5-49 Transfer Integral Tool 5-51 Data before Deconvolution 5-52 Deconvolved Data 5-52 Deconvolved Data with Deconvolve Sum 5-54 Deconvolved Data with Deconvolve Unsel 5-54 Spreadsheet after a Deconvolution 5-55 Annotation Rotation & Shift Keys 5-56 Data after Annotation 5-57 Level Tool -- Contour View (I) and Colors View (II) 5-59 Zoomed view of data showing Data points 5-61 Spreadsheet Tool 5-65 Save Data File Window 5-67 Print Options Window 5-68 Presentation Manager 5-69 Ruler Links (Links) 5-73 Ruler Limits 5-74 Ruler Links (Y Scale) 5-75 Presentation Manager (Preview) 5-76 Simple Mode 1D Processor 5-78 Data Slate 6-1 Vertical Data Slate Views 6-3 Horizontal Data Slate Views 6-4 Box Data Slate View 6-4 Data Overlay 6-6 Print Options 6-8 Resulting File Window 6-11 Connection Tool after and before a Connection is Made 6-12 Geometry Tool 6-13 Data Slate Slicing Menu 6-16 Data Slate Slicing 6-16 Expand Options Menu 6-17 Data Slate Expand Display 6-18 Expand Size Selection 6-18 Open File 7-2 Empty nD Processor 7-3 nD Processor Window 7-4 X-Domain processing list 7-5 nD Process Data Destination Buttons 7-8 2D Phasing Tool 7-11
xi
2D Phasing Tool Region Display 7-12 2D Viewer - Contour Mode 7-13 Mesh(a), Surface(b), Stack(c), and Image(d) Modes 7-16 Level Tool 7-18 Data with too few (only topmost) contours selected 7-20 Data with too many contours selected (well into the noise floor) 7-20 Data with a sensible distribution of contours selected 7-21 Peak Pick Overlay 7-23 2D Peak Pick Display 7-24 2D Peak Multiplet with Fine Structure 7-25 Peak Grouping 7-26 Peak Melding 7-26 2D Integration. 7-27 2D Annotation 7-28 2D Spreadsheet 7-30 T1 Analyze Tool 8-4 Open Data for Processing Window 9-2 Empty 3D Processor Window 9-3 3D Data Slate 9-8 3D Viewer Right Mouse Button Mode Selection Menus 9-9 3D Viewer 9-10 3D Viewer - Slices 9-11 3D Viewer - Zoomed 9-11 3D Slicer with Overlaid Spears 9-12 3D View Control 9-17 Spectrometer Control Tool after Connection 10-3 Open Experiment File Tool 10-4 Experiment Tool 10-5 Experiment Tool Header 10-17 Adding Header Fields 10-23 Experiment Tool Instrument Section 10-24 Adding Instrument Parameters 10-26 Experiment Tool Acquisition Section 10-27 Experiment Tool Pulse Section 10-30 Pulse Display Widget 10-31 Set Array Parameters Windows 10-51
xii
List of Tables
Window Menu Functions2-4 Delta Console Tool Bar Icons3-4 Shim Tool Nomenclature 4-14 Data Slate Icons6-7 Connect Functions6-15 Relaxation Experiment8-2 Experiment Tool Icons10-5 Experiment Header Parameter Definitions10-10 Experiment Acquisition Parameter Definitions10-12 Experiment Pulse Parameter Definitions10-13 Header Process Information Options10-18 Header Flags10-19 Temperature Parameter List10-25 Scans Parameter Limits10-29 Eclipse Probe Code List10-33 GX, GSX and CPF Assignments 10-33 IRR Codes for Probes10-34 Multiple Buffer Phase Cycles10-41 RF Channel settings10-41 Time-shared Homonuclear Decoupling10-42 Noise Modulation Gating10-42 Amplifier Power Settings10-42 Combination Features10-42 PGX-300 Pulser Specifications10-44 Irradiation Modulation Modes10-47 Irradiation CodesC-1 Conversion Example for TH5 ProbeC-1 GX Decoupler Amplifier ControlD-1 Delta NMR software package componentsL-4
CHAPTER 1: INTRODUCTION
INTRODUCTION
DELTA is a graphically-oriented NMR data processing software package running on Silicon Graphics computer workstations. DELTA uses a mouse-driven graphical user interface with pull-down menus and icons to perform common NMR data manipulations and to control the Eclipse NMR spectrometer.
ABOUT THIS GUIDE

This DELTA NMR Software User's Guide provides a useful overview of DELTA. It covers basic 1D, 2D, and nD NMR processing and data acquisition (see Chapters 5 and 7). For more information about the Eclipse NMR spectrometer, please consult Chapter 4. Other chapters and appendices provide a wealth of information. The introduction to each chapter provides links to its important topics. For further information on specic features of the DELTA software, consult the Delta Users Reference and Online Help, or the Percival Reference Manual.
BEFORE YOU BEGIN

DELTA must be correctly installed and congured on your workstation or network. If the DELTA software does not run correctly, please consult your system manager. Refer to Appendix L, Delta V3.2 Software Installation and Conguration Instructions. You must have an account on the workstation that runs the software. Please see your system manager to set up an account for you.
SPECIAL SYMBOLS
Special attention: This symbol marks an important explanation of an operation or a function. Warning: This symbol indicates that the operation could seriously affect operation of the software or hardware.
FONT CONVENTIONS
File names which are part of the DELTA software are shown in Courier font (for example,.delta_configure). Courier font is also used to designate UNIX console input, sample file contents, and output from DELTA programs in a console window. DELTA commands and tools are shown in bold type.
1-1
Chapter 1: Introduction
References to other manual names are shown in Times bold italics. SGI commands and window titles are shown in Helvetica bold italics.
KEYSTROKE CONVENTIONS
Two modier keys are commonly used as accelerator keys or as keyboard shortcuts: The CONTROL key is abbreviated in this manual as CTRL, or represented with the ^ character used in all the DELTA menus. For example, CTRL-G or ^G means press the CONTROL key, then press the g key. Note that DELTA accelerator keys are never case sensitive, whereas UNIX commands are always case sensitive. CTRL-1 means hold down the CTRL key, and then press the number 1 key. Zero (0) is also spelled out (CTRL-zero) to avoid confusion with the letter O. The ALTERNATE key is abbreviated ALT in this manual. ATL-g means hold down the ALT key, then press the g key. Note that, in SGI Windows Menus, ALT+F1 means hold down the ALTERNATE key, then press the F1 key. The ESCAPE key is abbreviated in this manual as ESC. The SPACEBAR key is abbreviated in this manual as SPACE.
COLOR CONVENTIONS
When a color is mentioned, it is assumed that the DELTA software is running with the default color scheme. If you customize the color scheme with the Conguration Editor or by editing the.delta_configure le, the colors mentioned in the manual may not match your screen display. It is not advisable to change different color preferences to the same color. Doing so may cause parts of the display to be obscured by other parts whose color is the same. Displaying data using the same color as the background color is denitely not advised!
1-2
CHAPTER 2: USER INTERFACE BASICS

This chapter covers only the basic operation of the Silicon Graphics user interface as it pertains to DELTA. For additional information, consult the documentation that came with your workstation. Some window features may not be available or active in other software applications.
POWER-ON
Consult the Silicon Graphics documentation that came with your workstation to determine the location of the power switches for both computer and monitor. Before proceeding, make sure that the workstation and monitor are turned on.
LOGIN
Please refer to Figure 2-1.
DELTA-J
Figure 2-1. Silicon Graphics Login Screen To log onto the workstation: Double-click on the DELTA icon with your mouse:
A password box will appear on the screen.
2-1
Chapter 2: User Interface Basics
delta
Password:
Delta User
password input box
DELTA-J
Place the mouse in this box and type your password. If the password is correct, this window will open (see Figure 2-2). The following gures and pictures may look different on your screen if you are running a different version of the UNIX operating system on your workstation.
Figure 2-2. Silicon Graphics User Interface Screen (detail) Silicon Graphics provides you with a graphical user interface (GUI) in which you initiate and input instructions using the mouse and cursor position. This contrasts with the older style command line (text) user interface where all commands are entered by typing on a keyboard. The keyboard is still used for text input, but the location is selected by the mouse cursor. Another important characteristic of the Silicon Graphics user interface is that multiple windows display on the screen simultaneously. Each window may represent a separate program, or a different part of a single application. Windows may perform operations simultaneously. Windows may be iconied to recover screen space or to move a window out of the way.
2-2
Mouse and Keyboard
MOUSE AND KEYBOARD

All user input is made using the keyboard and the mouse. The mouse controls a pointer or cursor on the screen. The shape of the mouse cursor will change, depending on the mode. The mouse has three buttons: left, middle, and right. The left mouse button is the most commonly used button for selecting objects, although all three buttons are used in DELTA. Input Focus Because multiple windows can be displayed simultaneously on the screen, the user must understand the concept of input focus. The input focus, or active window, is determined by the position of the mouse cursor on the screen. To enter text or other keyboard input, the mouse cursor must be in the desired window and at the desired location in the window. As the mouse moves from one window to another, the window border and window title bar will change from a dark to a lighter gray color to mark the active input focus window. To click the mouse: Press down briey, then release the mouse button. The mouse button to use -- left, middle, or right -- may be specied. Use the left mouse button unless this manual species the middle or right mouse button. A mouse click is also called a single click. Certain operations may be performed by a double click -- two single clicks in rapid succession. The second click of a double click sequence is interpreted as an OK. For this reason, double clicks are commonly used to select les. Do not develop a habit of excessively clicking the mouse. The response time of the workstation may slow during times of high CPU loading. However, the Delta software will remember all the mouse clicks and all of them will be executed as time allows. Unwanted functions could be performed! To drag the mouse: Press the mouse button and hold it down while moving the mouse to a new location. Dragging the mouse is commonly used for repositioning and resizing windows on the screen. Keyboard Use the keyboard for all text input. The keypad may also be used for numeric input. Arrow keys may also be used for zooming and panning the NMR data. The keyboard function keys (F1 through F12) are also assigned to special functions inside the Delta software. Structure of a Window The basic structure of a window is shown in Figure 2-3. This gure shows the most commonly used parts of a window. For more detailed information, see Anatomy of a Window in the section Getting Started shown in the Index for Desktop Help. This can be viewed by selecting Desktop Help from the Help submenu in the standard Toolchest. (See the Toolchest section on page 2-6.)
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Window Menu Button Path Bar Drop Pocket Pathname Field
Window Title
Maximize Button Iconize Button
Recycle Button
Window Border
Scroll Bars
Figure 2-3. Basic IRIX Window Structure
WINDOW MENU BUTTONS

On the left top corner of the window is a menu button, shown in Figure 2-4. Click with the mouse to display a menu of window options. The menu will remain displayed after the mouse button is released. Click with the right mouse button in the Title bar to display the same menu of window options; this menu will disappear when the mouse button is released. Drag the mouse to the desired option, then release, to execute the selected function. The most useful functions are Raise, Lower, and Quit. Table 2-1: Window Menu Functions Select: Restore Move Size Minimize Alt F5 Alt F7 Alt F8 Alt F9 To refresh the Delta Console window. To move the Delta Console window. To change the window size. To turn the window into a postage stamp size icon. To size the window to ll the terminal screen. To position the window in front of the other windows. To position the window in back of the other windows. To close the window.
Maximize Alt F10 Raise Lower Close Alt F1 Alt F3
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Iconifying or Minimizing Windows
Note: If there is a key combination next to the function, the keyboard combination will effect the same operation. These keyboard combinations are called accelerator keys.
mouse click
Figure 2-4. Window Menu Button
ICONIFYING OR MINIMIZING WINDOWS

Figure 2-5 shows two symbols that appear on the right side of the window menu bar. Click on the small square icon to minimize (or iconify) the window. Click again on the small iconied window to restore it to the original size.
Minimize (Alt+F8) [or Iconifying]
Maximize (Alt+F10) [or Restore (Alt+F5)]
Figure 2-5. Minimized and Maximized Windows
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MAXIMIZING WINDOWS TO FULL SCREEN

Clicking on the large square shown in Figure 2-5 causes the window to ll the entire screen. The full screen window will cover all other windows. This button acts as a toggle switch. Click on the large square again to restore the window to the original size.
MOVING WINDOWS
The title bar of a window displays the name of the window. If you position the mouse on the title bar and drag the mouse while pressing the left button, you can move the window (visible as a red outline) to a new location. When the mouse button is released, the contents of the window will be redrawn.
RESIZING WINDOWS
Windows displayed on the screen may be resized by selecting the border with the mouse and dragging it to a new position (see Figure 2-6.) The border and corners of a window are called handles. If you put the mouse pointer on the border or corner of a window, the pointer will change. This means you have grabbed the handle, and may resize the window by dragging the mouse from this point.
Figure 2-6. Moving and Resizing Windows
TOOLCHEST
A list of programs and utilities is displayed in the upper left corner of the screen as illustrated in Figure 2-7. This menu is called the Toolchest. If you select a category, programs within that category will appear. Drag the mouse to select the desired program or utility. The contents of the Toolchest are controlled by the.auxchestrc or .chestrc le in the user's home directory. The default Toolchest setup le is /usr/
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Toolchest
lib/X11/system.chestrc. You should customize your own account by using the .auxchestrc le in the user's home directory. See Modifying the Toolchest in the section Customizing Your Environment shown in the Index for Desktop Help. This can be viewed by selecting Desktop Help from the Help submenu in the standard Toolchest. If the right mouse button is clicked on the screen background (any blank area of screen outside a window), a menu is displayed as illustrated in Figure 2-8. If the workstation has been congured by JEOL, the menu will allow you to open a UNIX terminal shell and to log out; other options may also be available.
Figure 2-7. Silicon Graphics User Toolchest
Figure 2-8. Selected Menu
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WORKSTATION SYSTEM USAGE

Each workstation has a utility program called gr_osview. This program, a performance monitor for the system, is shown in Figure 2-9. To start the monitor: select System Usage under the Programs option in the Toolchest. To close the monitor window: place the mouse in the window and press the ESC key. To move this borderless window to another position on the screen: place the mouse cursor over the gr_osview window and, while holding down the ALT key, hit the F7 key (ALT+F7). The cursor will change to a four-sided arrow. The red outline may now be positioned anywhere on the screen. A mouse click will place the window at the new position. To get the Window Menu (see Figure 2-4) for a borderless window: press the ALT key and click the right mouse button. Unlike other borderless utility windows, the gr_osview window can not be resized. For more information on the system monitor and gr_osview, consult the SGI documentation or the man pages for gr_osview.
Figure 2-9. System Usage Monitor
TERMINAL SHELL
A window containing a standard UNIX shell, as shown in Figure 2-10, can be created by using the Desktop - Shell command located under the Toolchest menu. The Shell may be listed as Unix Shell, or Shell (terminal), depending on the operating system version.
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Logout Window
Figure 2-10. Silicon Graphics UNIX Shell Window
LOGOUT WINDOW
To log out from the workstation: select Log Out from either the Background menu or the Toolchest menu.
A logout will ask for a conrmation shown in Figure 2-11. Select Yes to log out. All applications and windows will be closed on logout.
Figure 2-11. Silicon Graphics Logout Conrmation Window
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CHAPTER 3: GETTING STARTED ON DELTA

INTRODUCTION
This section will briey describe the fundamental operation of basic DELTA processing tools. It covers procedures for: starting Delta (page 3-1) running Delta from the Delta Console menus and icons (page 3-3) tailoring the look and feel of Delta using the Preferences Tool (page 3-7) managing les (page 3-15) converting les (page 3-17). The DELTA software program is composed of tools. Each DELTA tool uses one or more windows to process, analyze and/or plot NMR data. Each tool is built with widgets which offer you different ways of entering information or manipulating data on the screen. These widgets allow you to input parameters, select functions, execute processing, etc.
STARTING DELTA
After you have logged onto the workstation, do the following: 1. Start the application by selecting Delta under Programs in the Toolchest menu in the upper left-hand corner of the screen. Or Double-Click on the Delta icon in the GUI window. Double-click on the Delta icon
Note: If DELTA is not listed under the Toolchest, see your system manager or consult Appendix O, Section II. If DELTA is running over a network, start-up could be delayed slightly by network trafc. If the application does not start up, look under the UNIX Console window for error messages, or use the System Usage tool to monitor CPU performance. Note: When running DELTA from your desktop, if autoplacement is turned on in the Miscellaneous Page of the Preferences Tool, then the Delta Console window will open automatically. Note: Train yourself from the outset to give Delta clear signals. Delta responds to each click of the mouse. For instance, use a single click of the mouse to open a window (otherwise, Delta will read each signal and duplicate windows will come up).
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Chapter 3: Getting Started On Delta
Note: As a general rule, it is better to complete processing and analysis of the data before employing virtual geometry features.
Note: Extremely large data les can slow down Delta.
THE DELTA CONSOLE

When you launch DELTA -- in all cases except where a preserve location is specied in the.delta_configure le -- a red outline of the Delta Console (Figure 3-1) appears. To activate the window: Move the mouse to position the Delta Console window anywhere on the screen and click to open the window. The window can be repositioned at any time. The Delta Console window pull-down menus and icons are used to invoke all Delta tools. To activate either menus or icons: Place the mouse cursor on your selection and click. This section will not cover all of the Delta Console options. For a more detailed discussion, refer to the (See Delta Users Reference: The Delta Console on page 6-1).
Figure 3-1. The Delta Console Window
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The Delta Console Menu Bar
THE DELTA CONSOLE MENU BAR

Along the top of the Delta Console window frame is a selection of topics called the Menu Bar (Figure 3-2). The Menu Bar lets you use the mouse to select functions and tools using the mouse.
Figure 3-2. Delta Console Menu Bar Note: The User menu is for user-dened choices. It is described in Appendix E on page 41. Pull-Down Menus
Each topic on the Menu Bar has a pull-down menu like the one illustrated above. Click and hold the mouse on a Menu Bar topic to display its menu of choices. Consult the Help and Delta Users Reference Guide for a description of these menus (page 6-4). To select an item from a pulldown menu: Drag the mouse down the list (keeping the mouse button pressed down) to highlight the desired feature. If you have chosen an incorrect menu, simply move the mouse outside the menu and release the button. Accelerator Keys Also displayed in the pull-down menus are accelerator key combinations. Hit a key combination on the keyboard to invoke a tool or an option. The carat character (^) on an accelerator key in the pull-down menu indicates the CTRL key. For example, in the menu illustrated above, ^S means hit CTRL S to access the Presentation Manager.
TOOL BAR ICONS

Located below the Delta Console Menu Bar is a set of icons representing many commonly used functions. This area is called the Tool Bar (Figure 3-3). Each icon has a unique picture that represents the tool or function you may select by clicking the mouse button. Clicking on the icon changes its appearance to that of a button that has been pressed down. Many of the Icon functions duplicate the functions under the Menu Bar. Table 3-1 lists and describes the function of these icons.
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Note: Selecting any icon with the right mouse button will bring up a label identifying it.
Figure 3-3. Delta Console Tool Bar Table 3-1: Delta Console Tool Bar Icons Select: To open the NMR data into a Data Processor. The dimensional size of the data is checked and the correct processor invoked. See Chapter 5 for more information on using the Data Processor (page 5-1). Note: to start the 1D processor, you may either select this Icon or select the 1D Processor option under the Processors menu. To use the Data Slate to display and manipulate 1D, 2D, and 3D data. See Chapter 6 for more information on using the Data Slate (page 6-1). To use a Data Viewer to view NMR data. The window is sized to the dimensions of the data displayed. See Chapter 7 for more information on the 2D Data Viewer (page 7-13). To navigate the subdirectories Delta uses for different les. The File Manager also allows you to copy, edit, delete, and rename les. Open this tool to consult its online Help. To use the Presentation Manager to customize design of a printout of NMR data and to organize the different processing of one or more data sets. Open this tool to consult its online Help.
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Tool Bar Icons
Table 3-1: Delta Console Tool Bar Icons Select: To display parameters and the processing history for any data set. Open this tool to consult its online Help.
To use a Spreadsheet to display peak, integral and assignment information in table form. Open this tool to consult its online Help (page 57-1). To use the Connection Tool to create connections between different data sets. Use the axial reference scale to establish links. Any data sets, regardless of data point density, sweep width and eld strength, may be connected. Open this tool to consult its online Help (page 19-1). To use the Eclipse Spectrometer Connection utility to connect to, or monitor, a spectrometer. See Chapter 4 (page 4-1). To use on-line help. Help will display a picture of the tool with a brief description of its functionality.
To use the mouse cursor to nger text to cut from the selected data geometry into another window on the Delta console. Note: To clear an input box, double click the right mouse button. To nger and paste text from the selected data geometry on the Delta console to a preselected window. A Paste can also be performed by clicking the middle mouse button when the cursor is in an input box.
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EXITING DELTA
To exit Delta after completing measurement or NMR data processing: 1. Select Quit in the File menu. 2. The Conrm window opens, asking whether you want to quit the program.
Figure 3-4. Conrm window 3. Select OK. Note: If you decide not to quit the Delta program, click on the Cancel button.
ON-LINE HELP
Located on most tools in Delta is a help icon button, which connects you, via Netscape Browser, to a .MIF help le offering useful guidance on that tool. The contents of this help le are identical to the framemaker/.pdf version of the Delta Users Reference Guide. 1. To start on-line help for the tool currently displaying on Delta: simply click on the help icon, or select Help in the menu bar. 2. Use the scroll bar to scroll up and down in the le.
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Preferences Tool
PREFERENCES TOOL
Figure 3-5. Preferences Tool - Personal Page The Delta Preferences Tool allows you to change the parameters that control the look and feel of Delta. These parameters are kept in the .delta_configure le, which resides in the users home directory and is described in Appendix E.
Note: The .delta_configure le is not meant to be edited with the text editor, but with the Preferences Tool. Note: Most parameters take effect when they are changed, without restarting Delta. Every parameter listed in the Preferences Tool with a * next to its name is one that does NOT take effect until Delta restarts.
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To invoke the Preferences Tool: Select File, then select Preferences, from the Delta Console window menu bar. A screen containing personal information about the user will display. At the top of this screen are icons that enable you to go from one page to any other page (or if you prefer, you can use the Options menu to access one of these pages or to congure the printer.) Use the icons to select a page in the Preferences Tool:
Select: To return to the Personal Information Page illustrated above from any other page.
To turn to the Directory Page, which contains a list of available directories. To select Printer and printer options such as orientation (landscape or portrait), paper size, tessellates, and parameter location. To turn to the Data Page, which contains information and features specic to the data found in geometries.
To turn to the Geometry Page, which contains information and features specic to the display of the geometry. To change the Alternate Cursor selections.
To select colors for displays, widgets, etc. You may also elect to display icons in black and white and change color mapping defaults.
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Preferences Tool
Select:
To turn to the System page.
To turn to the Miscellaneous page.
To turn to the Delta Tools page.
To turn to the Processors page.
To turn to the Automation page.
Use the buttons at the bottom of any pages to save new parameters or restore a page to its original settings: Selecting:
Saves modied preferences to .delta_congure and exits.
Restores only the parameters on the current page to their original settings.
Restores all parameters to their original settings.
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Disregards the changes and exits the Preferences Tool.
Note: Click on any title on any page with the right mouse button to get a help label. To search in the preference settings and pop-up help for any keyword: Select Search in the Options menu. A search window pops up. Type the word you want to nd into the box marked Search: (geom was typed into the Search Tool window illustrated below) Select the Go button. The Search tool then returns a list of all preferences or popup help containing the keyword (see the example below): page, # of preference on that page, title and when the word appears in the online help, that line of help. Select the reference you desire -- Colors #5, below - and click on it to go directly to it.
Figure 3-6. Search Tool To change parameters in the Preferences Tool: Select a eld with your mouse, and: Type in a new value. Select a new value from a list that appears. Move the slider to increase/decrease a value. Toggle the ON/OFF button. To start the directory tool: Select . The Show Hidden Files button expands the directory tool to include le names. You can either select a le from the File list or type in a lename. Select Apply to set the preference to the current directory. You can also drag the directory to a destination by selecting the input box at the bottom of this tool.
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Preferences Tool
Figure 3-7. Directory Tool Sample pages from the Preferences Tool -- geometry page, data page, and misc page -follow. All pages of the Preferences Tool are discussed in detail in the online Help, See Delta Users Reference: Preferences Tool on page 45-1.
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Figure 3-8. Preferences Tool - Data Page
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Preferences Tool
Figure 3-9. Preferences Tool - Geometry Page
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Figure 3-10. Preferences Tool - Miscellaneous Page
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File Manager
FILE MANAGER
Deltas File Manager makes it possible to edit, compile, delete, move, copy, purge, inherit, or keep a processing history of les.
Tool Bar Directory Input Box Subdirectory List File List Box
File Toggle Buttons
Version Number List Box File Management Buttons
File Info File Input Box
Directory Hop Buttons
Figure 3-11. File Manager To invoke the File Manager:
Select on the Delta Console. Or, select the File Manager command from File Access in the File menu of Delta Console. Select a le using the list and input boxes. The Directory Input Box displays the current directory. If you want to see a different directory, you can type the name of the directory and the path to it in the input box, and then press the enter key. Subdirectory List Box lists all the subdirectories in the current directory.
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Note: if the Show Hidden Files option in the Options menu is toggled on, all the hidden directories will be listed as well. File List Box lists all files that are in the current directory. Version Number List Box displays all version numbers of the selected file. Use the Tool bar icons to call up these tools with the selected le in them: (in order) Data Processor, Spectrum Phaser, Data Slate and Data Viewer:
An appropriate tool will be opened based on the dimension of the selected le.
Note: click and hold the right mouse button on the icon to reveal the name of the tool. Use the buttons along the right hand side to perform File Management Tool operations. See Delta Users Reference: File Manager on page 27-1 for a description of this tool.
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File Converter
FILE CONVERTER
Figure 3-12. Data File Converter Deltas Data File Converter lets you copy a le from one format to another. See Delta Users Reference: File Converter on page 26-1. To invoke the Data File Converter: Select File Conversion in the File menu of the Delta Console.
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To convert data: 1. Select a le type button in the From column, then one in the To column to convert from the rst le type to the second selected. 2. A blue arrow points from the source le to the output le. Select: To choose the directory and name of the le you want to convert. You may also enter the name of a Percival data le directly into the input box. To choose the directory and lename to store converted data. You may also enter the name of the Percival data le directly into the output box. To start converting the data. To save the intermediate JEOL Generic les.
To exit the Conversion tool. Use the Options Menu: To toggle on/off automatic extension correction and the display of progress messages.
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CHAPTER 4: ECLIPSE SPECTROMETER CONTROL

INTRODUCTION
DELTA communicates with and controls the Eclipse NMR spectrometer through several separate windows and tools. This section provides an introduction to these tools, and examples of basic NMR spectrometer control. This chapter discusses the following tools and processes: Spectrometer Control, page 4-2 Sample loading, page 4-9 Experiment and Queue management, page 4-21 Experiment, page 4-24 Experiment Automation, page 4-34 Automation Queue, page 4-37 Automation Editor, page 4-39 Sawth (Lock signal display), page 4-43, and View Tool (Real-Time monitor display), page 4-44. Note: To close any window: use the pull-down menu in the upper left corner or press the ESC key while that tool is the input focus.
SPECTROMETER TO HOST WORKSTATION COMMUNICATION

All communication from the workstation to the Eclipse spectrometer uses Ethernet using the TCP/IP Protocol. This means the user may establish and control an Eclipse NMR spectrometer thousands of miles away from the workstation. This distributed network has many benets for multi-user environments. Several different users from separate workstations can connect to the spectrometer to submit experiments or to retrieve data. Remote connection can even be established through a terminal emulator, or through X window emulation. The Eclipse NMR spectrometer has a complete UNIX computer embedded inside it. That computer is assigned a TCP/IP node address and name. This node name is what displays when the Spectrometer Control Tool is started.
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Chapter 4: Eclipse Spectrometer Control
SPECTROMETER CONTROL TOOL

To invoke the Spectrometer Control Tool:
1. Click on this icon in the Delta Console window
Figure 4.0-1. Delta Console Window or select Acquisition, then Connect, from the Delta Console Menu Bar. The Spectrometer Control Tool, from which all spectrometer functions and controls may be accessed, opens.
SELECTING A SPECTROMETER
When you start the Spectrometer Control Tool, its display screen lists all available Eclipse NMR spectrometers on the network (see below). If you have a single Eclipse spectrometer, only one node name is displayed
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Selecting a Spectrometer
Figure 4-1. Spectrometer Control Tool Use these Spectrometer Control Tool function buttons (Figure 4-2): Info to get information about a particular spectrometer (page 4-3), Connect to connect (page 4-4) or Monitor to monitor a spectrometer (page 4-6), Unlink (page 4-7) to terminate connection to a spectrometer, or Free (page 4-7) to ping the network for the status of the spectrometers.
Figure 4-2. Spectrometer Control Tool Top Buttons Select:
to display the contents of the machine.info spectrometer (Figure 4-3).
le from the currently selected
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Figure 4-3. Spectrometer Control Tool Info Display Select:
after rst selecting a spectrometer, to connect to a FREE spectrometer, and to gain ownership of the spectrometer and control of all its features. Depending on Ethernet trafc, it may take several seconds to establish connection. During this time, the workstation is uploading parameters from the spectrometer. The spectrometer name will be displayed in reverse video. If connection is successful, the message Connect is displayed at the top of the window, as shown in Figure 4-4.
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Selecting a Spectrometer
Figure 4-4. Spectrometer Control window after connection of the workstation and spectrometer After data collection, the data is automatically uploaded to the workstation if the spectrometer connection is valid. The data is placed in a le specied by the lename string in the experiment header. If the connection does not exist, the data is retained on the spectrometer for a time specied in the machine.config le. The next time a connection is made to the spectrometer, the data is automatically uploaded. If the process line in the experiment header contains a valid processing program, the program is invoked. Note: Connection to a spectrometer is necessary prior to scheduling any spectrometer activities. Default Spectrometer Connection Each user in the.delta_configure le has a Default instrument string. This string is the name of the spectrometer to which Delta will automatically try to connect when the Connect command is given. This string may be changed with the Preferences Tool. Note: In locations with only one spectrometer, the system is usually set up to connect to the spectrometer automatically after clicking on the icon.
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Select:
after rst selecting the spectrometer, to monitor (or observe an experiment on) a spectrometer already in use by another user. The Spectrometer Control Tool changes to look like Figure 4-5. Note: Only one user can connect to a given spectrometer at a time. However, users from other workstations can monitor the status of the spectrometer. A user can submit experiments while monitoring the spectrometer. However, those experiments are held in the experiment queue until the current user unlinks.
Figure 4-5. Spectrometer Control Tool in Monitor Mode
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Spectrometer Control Tools
Select:
to terminate connection to the spectrometer. Unlink is used to terminate both the Connect and Monitor connections.
to ping the network for the status of all Eclipse NMR spectrometers. The node names will be listed in the Spectrometer Control Tool window. Console mode In console mode -- which acts like a spectrometer superuser -- you have exclusive right to the spectrometer and can do any of the following: remove any job from the queue, change experiment priorities, write system shim les, etc. To connect to the spectrometer in console mode, select Tools-Mode-Console to bring up a window into which you enter the password. When a user connects as console, the Spectrometer Control Tool displays this information in the top window, which would read: console: nodename not connect:nodename
SPECTROMETER CONTROL TOOLS

Once you have successfully connected to the spectrometer, you may then select from various spectrometer functions and tools using the bottom row of buttons on the Spectrometer Control Tool (Figure 4-6). Most importantly, they make it possible for you to load a sample and to run an experiment. More information on any one of these tools can be found by rst opening the tool, then consulting online Help.
Figure 4-6. Spectrometer Control Tool Lower Buttons
Select: To load a sample, lock it, spin it, adjust its shims, etc.
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Select: To select an experiment, and to modify its various parameters (header, instrument, acquisition, and pulse). To open the automation window that lets you automate collection and processing of NMR experiments. To activate the swept lock signal display.
To activate the Real Time monitor display tool. Note: Once in this View Tool, you must select the View Vector button to activate it. To copy data from spectrometer to workstation while data collection is in progress.
Select:
to start the queue.
to stop the queue. (For a full listing of menu functions in this tool, consult page 56-5).
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Spectrometer Control Tools
SPECTROMETER CONTROL TOOLS

The Spectrometer Control Tools -- Sample, Experiment, Automation, Sawtooth, View and Copy -- are described in order here.
SAMPLE CONTROL TOOL
Figure 4-7. Sample/Shim Tool Select:
to display, in the Sample Control Tool (Figure 4-7) all the following: magnetic eld strength in Tesla
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cryogen level display, liquid He and N2 physical sample state (Load/Eject) sample changer slot (optional) sample spinning state and rate variable temperature state lock solvent lock control shim controls, and lock level.
To use the Options menu: Select Options Verify on System Shim Modify To ask for verication before modication of the system shims. Load Shims from Data File To get the shims by clicking on an open data le and load them into the Sample Control Tool. To set up a sample: 1. Set the sample tube (with the sample in it) in the spinner and adjust with the depth gauge. See your NMR administrator for the proper alignment procedure. Note: When inserting a sample tube into a spinner or removing it, do not apply excessive force to the sample tube wall. If it is difcult to smoothly insert or remove the sample tube, warm up the spinner by wrapping it up in your hand. This causes the spinner to thermally expand, ensuring easy insertion and removal. Warning: Never place an empty spinner into the magnet. 2. Check that the air is owing by holding your hand over the sample-insertion port of the magnet. If no air is owing, DO NOT insert the sample tube into the insertion port of the magnet. Another sample may already have been inserted or there might be a problem with the air system. 3. Put the spinner containing the sample tube into the sample-insertion port of the magnet and gently release it. The sample oats on compressed air. To load samples: Select:
L to load a sample; E to eject a sample in order to load a new one.
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Sample Control Tool
If the ask appears full
, and a green light appears above the Sample
Load Icon
, then a sample is already loaded in the magnet.
The bar above been ejected.
will turn yellow while the sample is being ejected, green when it has
The ask is empty when there is no sample loaded, or when the loaded sample has been ejected. When ejecting a sample, be sure to remove the sample from the insertion port on the magnet. Then, to spin the sample and update the display to the new spin rate:
Click on the Spinner
The sample spinning can be monitored by watching the picture of the top in the Spinner:
The top will be upright when the sample is spinning. It will topple over on its side when the spinning has stopped. Note: the sample may start spinning automatically, and can be turned OFF by
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selecting ejected.
. The spinner will always turn off when the sample is
Then, to control the temperature:
To turn temperature control ON, select:
To turn temperature control OFF, select:
To keep the temperature ON even when the sample is ejected, select: (otherwise, the ON icon will automatically turn to OFF when the sample is ejected). The re blazes when the temperature control is ON. It dies out when it is OFF Next, select the lock solvent from the Solvent scroll list.
(e.g., in Figure 4-7, CHLOROFORM-D was selected). The list of lock solvents is contained in the solvent.def le on the spectrometer. It is an ASCII le that is modiable with a text editor. Click on the automatic NMR lock and shim icon: .
When the NMR lock and shim are complete, LOCK ON and IDLE will be displayed.
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Sample Control Tool
Figure 4-8. Lock Control section displays the NMR-lock level Note: to manually shim the sample, use the mouse to maximize the lock level in the shimming section of the Sample tool (see Figure 4-9). Lock level indicators coarse ne
Figure 4-9. Set the axis for shimming The magnetic eld strength, appearing in a display-only eld in the Sample Tool (see Figure 4-7), is very important to spectrometer operation. All frequencies in Delta are automatically referenced from the nucleus name (Proton, Carbon13, etc.) For each nucleus a gyromagnetic ratio (gamma) reference value is stored in a le (gamma.def) on the acquisition system. The software multiplies the gamma value by the magnetic eld value to calculate the transmitter frequency. This calculated value also serves as the chemical shift reference position for each nucleus. Thus, an internal reference (e.g. TMS) is not required. This same method works for both Hz and ppm scales. The chemical shift of all peaks are calculated in this way. The gamma value should never need to be changed. However, samples prepared in mixed solvents, or solvents with high ionic strength, or samples run at variable temperature may cause the solvent peak to deviate from its expected chemical shift (ppm). In these cases, an internal standard may be used. Shim Tool Controls Shimming serves to homogenize the magnetic eld surrounding the sample. The Shim Tool Controls display the shim and lock controls.
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Table 4-1: Shim Tool Nomenclature Shim Function Magnetic field offset Spinning shims: Z1 Z2 Z3 Z4 Z5 Z6 Nonspinning shims: X XZ X2 X2Z XZ2 Y YZ Y2 Y2Z YZ2 X ZX X2-Y2 Z(X2-Y2) Z2X Y ZY XY Z(XY) Z2Y X ZX C2 ZC2 Z2X Y ZY S2 ZS2 Z2Y Z1 Z2 Z3 Z4 Z5 Z6 Z1 Z2 Z3 Z4 Z5 Z6 Eclipse name Z0 GSX name FILDC Spherical harmonic ZO
Note: All matrix shims systems have Z5 and Z6. These shim values are user adjustable in Eclipse +. Some systems may have X3 (C3), Y3 (S3) non-spin shims. The shims are displayed in groups of 4 on the Shim Tool Controls. Below each shim name is its current value and a button pad for shim adjustment. Different groups of shims may be displayed by clicking on the shim list. The 4 individual shim readouts may also be changed independently by clicking on the shim name.
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Sample Control Tool
Loading Shim Files Shim files for the Eclipse NMR are stored on the acquisition computer system. Because of this it is very easy to reset the shims to a known state. It is also convenient for the system manager to maintain the default system shim file. Individual users may also keep their own private shim files without disturbing the system shim files. Loading System Shims Select:
then magnet.
to load the default or system shims for the current probe in the
Reading in/saving the system shims generates acknowledge windows (Figure 4-10) if the Verify On System Shim Modify option under the Option menu is checked.
Figure 4-10. System Shims Acknowledge Window The system shim files are maintained by the system administrator. You must have Console privilege (i.e. the password) to overwrite the system shims. The system shim files are maintained in the /eclipse/probes directory on the acquisition computer. The default shim files are stored by probe code number. There may be only one system shim file per probe. The system shim files are written in ASCII format.
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Loading User Shims Select:
then to load a shim file from your own directory. Select the shim file from the Open Shim File window (see Figure 4-11).
Figure 4-11. Open Shim File window Select:
to save a user shim file back to the directory. Select the shim file from the Save Shim File window (see Figure 4-12)
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Sample Control Tool
Figure 4-12. Save Shim File window Select: to print the shims.
to upload current shim values to Delta to ensure the Spectrometer shim values and Delta shim values are synchronized. When you do this, a message box comes up:
The Lock Level Meter Located just below the center of the Shim Tool is the lock level meter (Figure 4-13). The top half gives the coarse reading, the bottom half the fine reading. Directly below is the numerical lock signal readout. By manually adjusting the shim controls located below the meter, you can optimize the amplitude of the lock signal.
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Figure 4-13. Lock Level Meter (Minimum 0, Maximum 4095) Locking the Spectrometer The lock system may be activated from the Sample Tool Lock Control (see Figure 4-14).
Lock Status Shim Status
Figure 4-14. Lock Control
Figure 4-15. Gradient Shim and Lock Buttons The NMR lock system uses the NMR signal from a 2H nucleus in the sample to lock the magnetic field frequency. This stabilization uses the Z0 shim coil to counteract any change or drift in the magnetic field during the experiment. The lock signal amplitude is also used for shim adjustment. A more homogeneous magnetic field will produce a higher amplitude of the lock signal. The Eclipse NMR lock system requires that the sample have 2H, usually in the form of the solvent, such as Chloroform-D, Benzene-D6, Acetone-D6, etc. The list of lock solvents is contained in the solvent.def file. The spectrometer may also be run in unlocked mode for samples without 2H or for performing 2H NMR spectroscopy, by selecting no solvent in the sample tool solvent list. There are two things that must be done for the machine to select the correct parameters from a probe le with two entries for 2H: 1) the module_config line in the experiment must specify the "lock_switch" option. This causes the pulse compiler to actually configure the head_amp to use the lock switch device.
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Sample Control Tool
2) The machine.wiring file must specify which head_amp circuit is connected to the lock_switch. This is done by putting a line like the following in the machine.wiring file: "HEAD_AMP(1).out_rf => LOCK_SWITCH(1).in_rf; (where head_amp(1).in_rf is connected to an LF amp and head_amp(1) actually is connected to a physical lock switch.
Select: To turn on the lock channel circuits. If the spectrometer is in resonance with the lock, it will lock. The lock on button does not sweep the field to find a lock signal. To turn off the lock channel circuits. Note: this does not turn off the 2H oscillator for 2H spectroscopy. To turn on the lock circuits, increase the lock power and gain, and sweep the field to find a lock signal. After it locates a signal, the lock power and gain are returned to standard levels. To perform autolock and shim.
To perform gradient shim.
To perform gradient shim and lock.
Lock State Shim State Gain
To display the current lock status. Red is OFF, yellow is WORKING, and green is ON. To display the current shim status. Red is OFF, Yellow is working, and Green is tracking based on the group selected. To adjust the gain of the lock receiver, set from the solvent.def file. Autolock will adjust the gain to find the lock signal.
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Select:
Level
To adjust the lock channel power level, set from the solvent.def file. Autolock will adjust the level to find the lock signal. To adjust the phase. It is set from the shim le. The phase is a characteristic primarily of the probe and of any RF lters in the lock channel. The lock phase may change when the dielectric constant or ionic strength of the sample changes substantially. To adjust the offset. It is loaded from the solvent.def file, the Lock Offset is the frequency offset necessary for the 2H lock signal to set TMS to 0 PPM.
Phase
Offset
Monitoring shims and lock signal level and record settings The spectrometer constantly monitors the shims and lock signal level and records settings corresponding to the highest lock signal level. Select: To clear the previous best shim values.
To restore the shim values corresponding to the highest lock signal level.
The standard autoshim invoked by the spectrometer is Z1, Z2. However, many other combinations are available. Click and drag on the autoshim input box to activate another autoshim combination. If the autoshim is stopped before completion, the spectrometer will execute a Lock On. The Lock On will affect the lock level and gain values, but will not affect the shim values.
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Queue Management
QUEUE MANAGEMENT
The Eclipse spectrometer is run as a queued device, that is, multiple experiments may be submitted to the spectrometer. The spectrometer queue has several modes - Owned, Running, Halt, Free, and Waiting. The queue can be altered only from inside the users account. Each job or experiment in the queue has a priority level. The priority ranges from 0 (lowest) to 255 (highest). The default priority is specied in the queue.priorities le on the spectrometer. As a user you can change the priority of your own jobs, but only to a lower priority value. Someone with Console privilege can change the priority of any job.
Queue Mode Owned
Queue Control State When you activate the Connect function and the instrument is free, you own the queue. Although others may submit experiments (the experiments will be held in the queue), only the connected user's experiments will execute. The normal state when another user is running an experiment. The queue is stopped. When the queue is restarted, all experiments will resume. The queue is free. An experiment is pending and waiting for user input.
Running Halted Free Waiting
The Queue menu on the Spectrometer Control Tool has four options useful in queue management. Select: Start to resume a stopped queue. Stop to stop the spectrometer from running jobs. Reschedule to reschedule a selected job to the end of the queue. Delete to erase the entire experiment queue except currently running jobs. When an experiment comes to the top of the queue and is ready for execution, the spectrometer checks the sample name currently in the magnet against that of the new experiment. If the sample ID is the same, the experiment executes without a pause. However, if the sample ID does not match, or if no sample ID was specied, the experiment will pause and display a message box on the screen (Figure 4-16). In this case, you must select GO.
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Figure 4-16. Acknowledge message window An experiment pending in the queue will resemble the one in Figure 4-17. Notice the- on the top line.
pending
Figure 4-17. Spectrometer Control with Experiment Pending After selecting the experiment, and selecting Start from the Queue menu, the queue will resemble Figure 4-18. Notice the- has changed to a*.
running
Figure 4-18. Spectrometer Control with Experiment Running Experiment Data
Priority Each experiment has a priority ranging from 0 to 255. A user can change priority only to a lower status. The Console has privileges to change any priority.
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Queue Management
Slot The slot parameter is used only with a sample changer. Job Start Time Normally, experiments are placed in the run queue immediately after submission. However, an experiment may have a delayed start time. The Job Start Time is the time the experiment is placed in the run queue, not necessarily the time when it starts running. Additional Experiment Information If you double-click on an experiment in the queue list window, an information window will appear on the screen (Figure 4-19). The window contains information related to the experiment.
Figure 4-19. Experiment Information Window 4. If the parameter you want to conrm is not in view, scroll the screen by clicking on the up L or down Marrow until it appears. 5. To close the window, click on the Finished button. Note: You cannot change an experiments parameters once it is in the queue. Deleting Queue items Deleting a specic queue item You can remove a measurement from the queue as follows: 1. Click on the item you want to delete from those displayed in the Spectrometer Control window. The specied queue item becomes highlighted. 2. Click on the STOP button in the Spectrometer Control window. The conrm window opens, asking whether or not to delete the queue item.
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3. To delete the queue item, click on the OK button. Deleting all queued experiments 1. Move the mouse pointer to Queue in the tool bar in the Spectrometer Control window, and press and hold down the mouse button. A pull-down menu appears.
2. Move the mouse pointer to Delete and release the mouse button The Conrm window opens, asking whether or not to delete all the queue parameters.
To delete all the queue parameters, click on the Ok button.
EXPERIMENT TOOL
The Experiment Tool stores, creates, and compiles the pulse sequence and parameters. The Experiment concept combines pulse sequences and parameter les into a single unit. The entire experiment is stored with the resulting data and may be extracted and re-run. An experiment has four basic parts: Header, Instrument, Acquisition, and Pulse. From the Spectrometer Control Tool, it is possible to run an experiment. For information on how to write and modify experiments over and above what the following section provides, please consult Experiment Tool and Eclipse Experiment Programming on page 10-1, 1D NMR Measurement on page 4-
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Experiment Tool
1, and 2D NMR Measurement on page 5-1. Experiment Selection In the Spectrometer Control window, select :
to access the Open Experiment window (Figure 4-20). You may use this window to select an experiment.
Figure 4-20. Open Experiment Tool Local Experiment Directory Select:
to list your local experiments. The user's local experiments directory is specied by the Experiments string in the.delta_configure le. Global Experiment Directory Select:
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to list the global experiments. The system global experiments directory is located as a subdirectory in the Global string in the.delta_configure le. In this directory, the standard les supplied from JEOL are stored. Its les cannot be changed. These Experiment les contain the measurement modes, standard measurement conditions, and processing operations to be carried out. Loading an Experiment The experiment loads as a single window containing all parameters necessary for a particular experiment. It is divided into four parts, which you can either select with icons or scroll to. The Header Section The Header section (Figure 4-21) is used for the sample_id, filename, comment, etc. However, it has two other major functions. First, the process section of the Header species what processing, if any, is to be done with the data after collection. Second, the Header section has experiment ags. The experiment ags control various spectrometer and data collection features. The experiment ags can be added dynamically by clicking on the Header button. (See Adding Header Flags and Parameters Dynamically in Chapter 10 or page 4-3 in the Delta Tutorial for more detail.) The parameters added will be used for the current experiment only.
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Experiment Tool
Figure 4-21. Experiment Header Section Set Hints in the Options menu to show buttons to set experiment parameters. Click on the parameter name to bring up an edit window. Not all parameters have an edit window. Select the Edit button to customize data handling: The Set process window allows you to customize the way the data is treated after the experiment is completed (see Figure 4-22).
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Figure 4-22. Set Process Window To edit the process command line, click on the Edit Button to bring up the Set Process window which allows you to set the process parameters for the experiment. The input box lists the name of the program or macro to be invoked when data collection is completed. If it is left blank, the data is simply written to disk. Use the horizontal row of buttons at the top of this tool to start the processor appropriate to the selected data:
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Experiment Tool
Select: Process_nDimensional . . . Process_Interactive_ Global To process data from the source specied. Process_Interactive brings up the process 1D or nD window, Process does not. Process_Local will (behind the scenes) process the data le using the supplied processing list in the local processing list directory. Process_Interactive_Local will pop up the window and load the processing list found in the local processing list directory. Process_Global (behind the scenes) will process the data found in the global processing list directory. Process_Interactive_Global will pop up the window and load the processing list found in the global processing list directory. To send collected data to a process you have ngered. To type a user-dened processing program. To opens a window allowing you to specify the userdened or global processing list. To remove the processing list lename from the command. To place the command into a process parameter. To cancel the setting.
Send_data_to_nger Other () Get Process List Clear Processing list Accept Cancel
Process lists may be created directly from data processors. The Instrument Section The Instrument section (Figure 4-23) contains instrument-related hardware conditions. A complete listing of instrument parameters is given in Appendix B, Instrument Parameters, or can be viewed using the Params button on the Spectrometer Control Tool. To add additional instrument parameters: Click on the Instrument title (a button may or may not be visible). (See Adding Instrument Parameters Dynamically on page 10-26, or page 4-4 of the Delta Tutorial.) The parameters added will be used for the current experiment only.
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Figure 4-23. Experiment Instrument Section The Acquisition Section The Acquisition section (Figure 4-24) contains the acquisition parameters, providing information about the NMR frequencies, sweep widths, data points, etc. In certain parameter elds, you may enter only a single numeric value (in some cases, multiple values). See page 4-5 in the Delta Tutorial for a discussion of setting Acquisition parameters.
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Experiment Tool
Figure 4-24. Experiment Acquisition Section The Pulse Section The Pulse section (Figure 4-25) contains the virtual parameters needed for the pulse sequence. See Pulse Section on page 10-29 and page 4-6 in the Delta Tutorial for more detailed information.
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Figure 4-25. Experiment Pulse Section View pulse sequences by clicking on the Pulse title. A pulse viewer will pop up on the screen (Figure 4-26). Any changes made to a particular experiment can be saved for future use in the users home directory. To do this, select Save from the File menu.
Any changes made will NOT affect the default values from the global directory.
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Experiment Tool
Figure 4-26. Pulse Viewer
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AUTOMATION WINDOW
To open the Automation Tool: (Figure 4-27), Select:
Figure 4-27. Automation Tool
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Automation Window
Use the Automation Tool to automate NMR experiments. With this tool, you can collect, process and present data. It lets you submit a series of experiments, or pass parameters from previous experiments for use in a subsequent experiment. When the Automation Tool is opened, it automatically checks the local template directory for the default le -.delta_automation.auto. If this le is not found in the local directory, the global template directory will be checked. If no default le is found in either directory, the tool will be opened and left empty.
Select: To load a new methods le and remove all currently loaded method les.
To load a new methods le without removing currently loaded method les.
To show the Automation Queue (page 4-37).
To hide the Automation Queue.
To invoke the Automation Editor (page 4-39). Note: If the single line separating the experiment buttons is clicked, it will change into a double line. This will cause the experiment le right below the double line to be loaded into the Automation Editor when it is opened. To inform the instrument that it is OK to run experiments.
The File menu (see also page 14-4) lets you load (or remove) a methods le, save it as the default le, look at the automation queue, or start the Automation Editor (Figure 4-30). Use the File menu also to access the LC-NMR Method Queue. This tool is described in the Users Reference Guide (study this material in LC-NMR Method Queue on page 34-
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1). The Sample menu lets you load or eject the sample. Note: The rst time a sample ID is used in an experiment automation, a message box will pop up to remind you to load the sample. Click the OK button after loading the sample to continue the experiment. To run an experiment, rst ll in the following information: Filename Supply a sample lename. In some cases, where there is no Sample ID eld, this parameter is used for the Sample ID as well. Enter your comment for the sample. Select a number for the sample changer slot for the next experiment. Use zero for no sample changer. Select the temperature desired. Select from Temp On/Temp Off to turn on/off the automatic temperature control. Select a solvent from the list. When an automation is complete, e-mail notication will be sent to the addresses specied. Shows if theres a sample loaded in the spectrometer. Gives the current spectrometer temperature. Gives the current spectrometer lock status. Select from the method buttons at the bottom of the screen. Doing so will submit all experiments in that method to the automation queue. Use the right mouse button to see the help on that method.
Comment Slot Temp. Set Temp. State Solvent Notify: Sample Status Curr. Temp. Lock Status Method buttons
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Automation Window
Automation Queue
Figure 4-28. Automation Queue Window The Automation Queue window lists experiments in the order they were submitted. The rst experiment in the queue will be highlighted in green (if, for any reason -- e.g., a sample with the wrong lock solvent is inserted into the spectrometer -- this experiment will be bumped, it will appear in red at the bottom of the list.) The scissors button lets you cut a single method from one place in the queue, to paste it (using the paste icon) in another. Use the Remove button to remove a selected experiment from the queue. You can also save a particular queue to your home directory, by selecting Save Queue in the Options menu. Options-Print Queue lets you print the contents of the queue.
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AUTOMATION CONSOLE
Spectrometer control Sample monitoring
Sample Preparation
Method Selection
Figure 4-29. Automation Console The Automation Console (Figure 4-29) acts as a dummy terminal to simplify data collection for users who don't need the full functionality that the Delta Console provides. It combines features of spectrometer selection and control with automation features and sample monitoring. For a more complete description of this tool, see Delta Users Reference: Automation Console on page 15-1 (or online help). See also LC-NMR Method Queue on page 34-1. Essentially, it combines features of the Spectrometer Control Tool, the Sample Control Tool and the Automation Tool. Note: In order for this tool to come up automatically when you start up Delta, the DELTA_CONSOLE preference needs to be set by the system administrator to automation_console, or it needs to have automation_console as an element in a set of elements (see Appendix E in the Delta User's Guide). Note also that this tool has a user-dened menu option described in Appendix E, p. 46.
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Automation Editor
AUTOMATION EDITOR
Figure 4-30. Automation Editor To invoke the Automation Editor (see Delta Users Reference: Automation Editor on page 4-39): Select Automation Editor from the File menu of the Automation window. Or Select Automation Editor from the Acquisition menu of the Delta Console. In this scrolling window you can edit any of the parameters for automatically running all the experiments in any of the methods in the automation template le. Its usage is more fully detailed in on-line help or see Delta Users Reference: Automation Editor on page 13-1.
Select:
To open an automation template le.
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Select:
To open a new automation template le and combine it with the current automation template.
To save the automation template le.
To bring up the Edit Sample window to edit the default sample list. Note: The parameters entered in the Edit Sample Window will only be used if the select enumeration next to the parameters found in the sample section is set to Sample. To display the Dependency Graph of the experiments in a selected method.
To bring up the Presentation window to customize the way data les will be plotted after each group is run.
To jump to the Method section.
To jump to the Group section.
To jump to the Experiment section.
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Automation Editor
Select: To jump to the initialize/forward section.
To jump to the sample section.
To remove the selected item from the list and store the content in the paste buffer.
To paste the content of the paste buffer.
Methods for Customizing Automation It is important to understand the Automation Editor. As the ow chart below exemplies (see Figure 4-31), you can run multiple experiments and print their outputs tailored to your needs with a single click of a button. You can also forward parameters from a previous experiment in a group to successive experiments within the same group. Passing (or forwarding) of information from one experiment to another is only permitted within individual groups.
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All experiments in one
Method name
PROTON
CARBON
2 DIMENSIONAL
Group name Exp. name
single pulse
homo_gated
13C
APT
DEPT
1H
13C
COSY
HETCOR
PRESENTATION
PRESENTATION
PRESENTATION
Figure 4-31. Flow Chart for an Automation Editor The Automation Editor allows you to generate methods to customize automation in a multi-user environment. This structure is reected in the design of the Automation Editor. With this editor you can cut and paste a method and all associated information into another automation le. A method consists of groups which in turn contain experiments. The method name identies its purpose in the Automation Tool. Name length is limited to 25 characters; truncation is automatic. Ctrl-click will turn the input box green and allow the user to change/edit the name. Alt-Click will deselect the item in the list box.
Groups ensure exibility, even from the quality control standpoint. Each group is capable of executing a Percival program upon its completion. There are three predened Percival programs that can be run: dept_automation --> automatic subspectra dept_lter {x,y,z,a}: where x,y,z,a are 13c, Dept 45, Dept 90 and Dept 135 respectively phase_automation --> phase of 2D phase-sensitive data. Experiments are executed sequentially. Each experiment must have an experiment le associated with it. In addition, the data le returned after completion of an experiment has to be processed if an output is required. The necessary processing list is placed in the eld that requests a process le. It is important to note that a single returned le can be processed using multiple process les.
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Lock Signal Display - Sawtooth
For automation in a multi-user environment, it might be necessary to reset the shims to a default value. The shim le eld accommodates this feature. From an automation point of view, it is recommended that this option be invoked only for the rst experiment in a group. Use Forward/Initialize to customize the parameters of an experiment at the time of execution. Any parameter you initialize will override the parameter in the experiment. This allows for changing instrument and user-dened parameters. For a list of common parameters, click on the parameter button. Forwarding parameters is of great importance when acquiring 2D data sets. For ease of use, the commonly used forwarded parameters are available as pushbuttons. In addition, the forwarded parameters can be constrained using >, >=, <, <=, Multiplier and Mod. Sample lets you control certain features so that they are non-modiable. As an example, temperature control can be disabled for the front-end user. If a value is: Runtime controllable, editing is allowed when submitting an experiment. Fixed, the parameter is not modiable. Sample. If a sample is specied in the group section it will use the value that is in the sample denition. For more detail, see Delta Users Reference: The Logic of Automation Editing on page 13-7.
LOCK SIGNAL DISPLAY - SAWTOOTH

Sawtooth derives its name from the wave form used to drive the Z0 shim. The shim coil sweeps the magnetic eld over the Sawtooth Range. If the lock signal is in the range, a signal will be observed. Often the Lock Gain and Lock Level must be increased to observe the lock signal. However, they may need to be lowered after the signal is located to prevent saturation. Select:
to activate the swept lock signal display. This display may be used to locate and observe the lock signal (Figure 4-32). Normally, it is not necessary to run Sawtooth on every sample unless there is a problem with the autolock function, or unless the sample lock solvent composition is unusual (i.e. 10% D2O, or mixed solvent). In Monitor mode, this function is not allowed. The Sawtooth runs a separate experiment that appears in the queue in the same manner as any other experiment. Because of this there will be a pause to download the pulse sequence and trigger the rst acquisition. Data will not appear in the SAWTH window until the rst acquisition has nished. It is possible to shim on the lock signal simply by using the Sample Tool while Sawtooth is running. Pressing the button marked Cancel Sawtooth will cancel
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this procedure.
Figure 4-32. SAWTH or swept lock signal display
VIEW TOOL
Select:
to activate the Real Time monitor display tool (Figure 4-33). This tool will display the current summed data from the acquisition processor. This data is shown in Real Time at the interval specied by the mod return parameter in the Experiment acquisition section. The View Tool display may not be able to keep pace if the data set is too large, the acquisition time and relaxation delay are too short, or if the network load is too great. Data is not lost in this case. The View Vector Speaker button must be pressed to activate the View Tools display. After 5 minutes of activity the View Tool will deactivate (gray-out) automatically. This feature is to prevent accidental overloading of the network when operators inadvertently leave the View Tool open. To reactivate the View Tool, press the View Vector button again. When the View Vector Speaker button is toggled to this setting hear the sound of a FID: Hear the data while you are collecting it! , you can
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View Tool
The View Tool may be used to shim on the FID with either the Shim Tool or the spectrometer sub-operation unit (i.e. knob box). Set the Repeat ag to TRUE in the Header Section of the Experiment Tool to do this. Under the Processing pull-down menu is an Abs Intgrl command. This option will calculate the absolute value of the integral and display the log10 of the integral. Under the Processing menu, you may apply several processing steps to the FID. Press the Process Vector button to display the current vector processed according to the check boxes in the Processing menu. When the display mode or processing mode is changed, the display will not update until the next acquisition vector is received. For more information, see Delta Users Reference: View Tool on page 63-1.
Figure 4-33. View Tool -- raw data
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Figure 4-34. View Tool - processed data
COPY
Select:
to copy data from the spectrometer to the workstation while data collection is still in progress. All the accumulated data will be returned. If the acquisition rate is too fast, Copy may terminate the experiment. Note also that you may control the availability of the Copy function, disallowing copy, by default, for automation experiments. To do this, select the allow_copy experiment header parameter in the header parameter list that pops up when you select the Header title in the Header window.
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CHAPTER 5: PROCESSING 1D DATA

INTRODUCTION
This chapter will cover the basic steps and an approach for processing one dimensional NMR data with Delta software using the 1D Processor -- including procedures for: Start-up (page 5-4) File selection (page 5-4) Processing list construction (page 5-7) Mouse Cursor (page 5-19) Level Tool (page 5-59) Data Geometry Options (page 5-60) Spreadsheet (page 5-64) Presentation Manager (page 5-69) Simple mode processing (page 5-78). A detailed walkthrough of 1D is found in the Delta Tutorial, beginning on page 4-1.
Figure 5-1. 1D Processor
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Chapter 5: Processing 1D Data
1D PROCESSOR
Use the 1D Processor (Fig. 5-1) to process one-dimensional data. This section will not cover all features of the 1D Processor. It will cover only the basic steps of 1D processing. For a more detailed discussion of menus and tools, see Delta Users Reference: 1D Processor on page 7-1. Since the Mouse Cursor Tool (page 5-19; and Delta Users Reference: Mouse Cursor Tool on page 4-1), Level Tool (page 5-59; and Delta Users Reference: Level Tool on page 5-1) and Presentation Manager (page 569; and Delta Users Reference: Presentation Manager on page 46-1) are used extensively in manipulating data in Delta, their usage in 1D Processing will be introduced briey later in this chapter; these tools are more fully described in the Delta Users Reference Guide. The 1D Processor will have two data display areas when the Show FID toggle in the Preferences menu is enabled: The upper area displays untransformed data. The lower area displays processed data. Icons (including user-redenable processing algorithms), menus and labelled buttons control the processing. The 1D Processor also has specialized widgets for phasing (P0, P1, PP in the lower right hand corner of Figure 5-4).
input area
output area
Figure 5-2. 1D Processor with untransformed and processed data
5-2
1D Processor
The 1D Processor display window format is controlled by the Show Tools and Show FID options under the Preferences menu on the menu bar. Show FID will show only the original data in the le; hence, if the le was saved with transformed data, the FID display area enabled by Show FID will not contain a FID, but the transformed data set! In addition, the 1D Processor Tool has two modes: a Simple Mode for basic push-button processing (page 5-78), and an Extended Mode for both basic and advanced processing. Default Start-up Mode You can set the default start-up mode for the 1D Processor by using the Preferences Tool. Normally, Extended Mode is the default start-up mode. But if the PROCESS_ONED.SIMPLE_MODE parameter in the .delta_configure le is set to TRUE, then the Simple Mode will be the default. To switch between Simple and Extended modes while running DELTA: select or deselect Extended in the Preferences pull-down menu from the 1D Processor Window Menu bar. To save the selected mode so that it is invoked the next time: choose Save Explicitly in the Preferences menu.
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1D PROCESSOR START-UP PROCEDURE

To load data into the 1D Processor: Select from the Delta Console Tool Bar, or Processors, then Process 1D (^1), on the menu bar. If you start the 1D Processor by selecting , the rst window to appear is an Open File Tool with the title Open Data for Processing (Figure 5-3).
Current Directory Name List of Subdirectories List of Files Directory Icons File Info Name of Selected File Figure 5-3. Open File Tool Window The Open File Tool
Input File Filter File Version Number
The Open File Tool Window has several parts: At the top left is the current directory name. Use the mouse to select and then edit this string. At the top right is the input le lter, a string that restricts the list of displayed les to those that match the lter. An * will show all les (i.e.,.DAT,.TXT, etc.). Use the mouse to select and then edit this lter. On the left side is the list of subdirectories in the current directory. The .. symbol is the next directory above the current directory. Use the directory icons to initiate data le selection:
File information and le name elds contain the specied information. The center column lists les in the selected directory. The bars to the right side of each column are scroll sliders. Use the mouse to scroll the display. The right column contains the le version number. Delta supports multiple le versions by appending a number to the end of the lename.
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1D Processor Start-Up Procedure
Delta never processes or destroys the original data set. Before any data set is processed, a copy of the data is made with the same lename, but a different version number. When you save a data le, the data is written to disk with the same lename, but the version number is incremented. Because some copies of the data are used and then deleted during processing, it is common to have gaps in the version number list. If you do not select a le version number, the most recent (highest number) version is assumed. To select a 1D data le from the Open File Tool: 1. Browse the directories to select the le to be processed. Select: To display all hidden les and subdirectories in the current directory. By default, these les are not shown. Click this icon once for local directory and twice for local home directory. The Open File tool will list the directory specied by the DATA entry in the .delta_configure le. Click this icon once for the global directory and twice for the global home directory. The Open File tool will list the directory specied by the GLOBAL entry in the .delta_configure le. 2. Choose a le from the list of les, and a version number from the le version numbers to the right. If you do not specify the version, the latest version (the one with the highest version number) is selected. 3. Click on the OK button. The Open Data for Processing window automatically closes and the1D Processor window opens. Note: If you decide not to load data, click on the Cancel button.
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1D PROCESSOR WINDOW - EXTENDED MODE

After selecting a data le from the list in the Open Data for Processing window and selecting OK, the red outline of the 1D Processor window will appear on the screen. Use the mouse to position the window, clicking the mouse button to place the 1D Processor window (Figure 5-4). You can change the position of the window or size it at any time using the mouse. The 1D Processor window title bar will then display the name of the selected data le. Selecting the Process 1D command from the Processors menu in the Delta Console will open a blank 1D Processor window with only Process 1D in the window title bar. You must then call the Open File Tool yourself. Note also that if you select a le of greater than one dimension, an nD Processor window will be required to process it. The nD Processor will be invoked automatically.
Data Source Radio Toggle Buttons
Figure 5-4. Extended Mode 1D Processor after Performing FFT and Phasing Note: For a quick reminder of any icon button function, simply select the button with the right cursor button.
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1D Processor Window - Extended Mode
Processing Lists This Processing List illustrates the basic concept of the Extended Mode 1D Processor. It takes the data from the input (upper) window area and outputs it, processed, to the lower window. For example, the data in the lower window of Figure 5-4 has undergone Fast Fourier Transform (FFT) and phasing.
Process List Source Radio Toggle Buttons
Open Processing List Save Processing List
List pointer ( ) Selected item Scroll bars
List display area
Figure 5-5. 1D Processing List Processing lists may be obtained in two ways: To recall a processing list from disk: Select File - Open List from the 1D processor menu bar. Then, in the same manner you selected a data le from the Open File window, select a processing list from the Open Process List window (Figure 5-6).
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Figure 5-6. Open Process List window
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The list you select will be read directly into the List display area illustrated above (Figure 5-5). Note: A Processing List may also be saved to disk. To build a new processing list using icon buttons and menu commands: Select processing algorithms - operators - from pulldown menus under the menu bar, and from the double row of icons. As you select them, they become part of the processing list. To select an operator from the menu bar: 1. Select a menu on the 1D Processor. 2. Holding the mouse button down, drag the mouse to highlight the desired option or command. Certain operators require that arguments be supplied. 3. Release the mouse button and the option will appear in the processing list. Note: Processing lists may also be edited by user-modiable macro buttons (the second row of icons). Note: 1D Processing Lists always end with the[display/phase] statement. This statement always appears at the end of the list and cannot be removed. To edit any processing list in the List Display area: Select from the set of pushbuttons in the upper right of the Extended 1D Processor. Certain buttons control how the processing list is assembled: Select: To apply the processing list to the input data each time a change is made to the processing list or the list parameters. Auto Process may be CPU-intensive, depending on the length and complexity of the processing list and data set. To apply the processing list to the input data and display the result in the output window. To place the next processing item at the end of the current processing list. Even if a processing step is highlighted, the next selected item will be placed at the end. To place the next processing item before the selected item. This allows you to insert new operations anywhere in the list. To change a selected (highlighted) item to the next item selected from the pull-down menu or the macro button.
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Select: To cut the selected line from the processing list. Note: Cut and Paste are local to the processing list.
To paste a cut item at the selected location in the processing list.
To clear the whole processing list.
To delete the currently selected (highlighted) item in the processing list. All items following the deleted item will be renumbered automatically.
Note: Any particular function should only appear once in a given processing list. When you add an item make sure that you delete any previous occurrences of that item. A Sample 1D Processing List You create a processing list (see below) by selecting processing algorithms in the order desired from the menus in the 1D Processor. For example, you might select: DC_balance from the Pretransform menu. Single exponential from the Window menu. FFT from the Transform menu. Machine Phase from the PostTransform menu. PPM from the Display menu. to process the data.
Then select
Extended Mode Icon Buttons - Top Row At the top of the 1D Processor are icon buttons used for retrieving, loading, saving, printing, and automatically processing data. This row is also used in the Simple mode. Note: DELTA can retrieve data from different sources. See below.
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Select: To open data les from disk. This is the most common data source.
To load a data le from another geometry.
Note: One or the other of these two buttons is always selected (depressed), so, in effect, these buttons toggle.
If the 1D Processor is already running, load new data by selecting either this Open File folder icon or Open File (Ô) from the File menu. The source of the new le is decided by which icon is depressed - the disk icon or the nger icon. Select this Open File Clear icon or Open Clear from the File menu to load a new 1D le and remove the current processing list. The source of the new le is decided by which icon is depressed - the disk icon or the nger icon. To export the current geometry into the Data Slate (see Chapter 6).
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Select: To save processed data to disk. This window will appear.
Figure 5-7. Save Data File window The lename will stay the same, the version number will be incremented by 1. To plot the processed le.
To print a spreadsheet with all the peak information.
To automatically peak pick the data.
To automatically integrate peaks by measuring and calculating a running sum for the area underneath selected peaks. To automatically peak pick and integrate the spectrum.
To compute the le statistics and update the geometry with the new le. These statistics include positive and negative threshold values, noise, baseline, minimum and maximum intensities.
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Select: To autophase the spectrum.
Extended Mode 1D Processing Icons -- Second Row The most common processing functions can be selected by clicking on the second row of icon buttons located at the top of the extended 1D processor. These buttons -- each of which has a default given in the table below -- may be redefined to related standard 1D processing functions by the user.
Note: It is also possible for the user to dene a macro to meet the special needs of an experiment set.
Select: To redene any macro, click on Dene, then on the macro icon. Select the new process(es) from the list of Operators. The new macro is memorized only for that session unless Save Explicitly is selected in the Preferences menu. You can use the buttons to cut from, paste to, append or insert into, or remove an operator from the list. Apply applies the change, Cancel cancels it. To remove stray zero frequency peaks that may be caused by a channel imbalance in the FID due to a difference in the DC Balance. To apply a Hamming window function to the le. This button can be reset to apply any of these Window functions: Double Exponential, Gauss, Hamming, Kaiser, Single Exponential, Sinebell, Sinebell Automatic, Sinebell (order 2), Sinebell (order 4), Sinebell Shift, Traf, Traf Modied, Trapezoid3. To perform a Fast Fourier Transform (FFT) on the le to transform the data from the time domain to the frequency domain. This button can be reset to include any of the Transform functions: FFT, Hilbert, IFFT, Maximum Entropy, Transpose.
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Select: To apply user-dened phasing. This button can also be redened to apply Automatic Phase and/or MachinePhase.
To correct for errors found in the baseline of frequency domain spectra. This button can be redened to apply any of these PostTransform functions: Base Correct, Base_correct (Interactive), DC Correct. To take the absolute value of the le and reduce the le to the size of the real only data. Alternatively, this button could be dened for the Symmetrize function. To translate the data into parts per million (PPM). This button could also be dened for Hertz or Automatic Reference rulers. To peak pick the data le. This same button can be used to apply Peak Pick/Integrate, Apply Integral or Print peak list processing to the le. To plot the spectrum and its parameter information. This is a predened macro button. Only operators from a predened set can be used in this macro (see page 5-10). To use a user-dened processing macro.
MENUS FOR EXTENDED 1D PROCESSING

This section discusses Pretransform (page 5-14), Window (page 5-17), and Transform (page 5-17) functions. PreTransform Functions The PreTransform menu contains various operations done before the FFT. Only two -DC Balance and Zeroll -- will be discussed here. Please consult the DELTA Users Reference Guide for a discussion of the other PreTransform menu functions (page 5-14).
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Menus for Extended 1D Processing
DC Balance The DC balance function calculates any DC (constant) offset between the real and imaginary data channels. An imbalance between the channels causes a center spike or zero frequency glitch in the transformed data. Zeroll The Zeroll function extends the data set with zeros by the number of times specified. All dimensions must be a power of 2 and will be automatically zerofilled to the next larger power of 2. Therefore the number of times specified should be a power of 2, i.e. 1, 2, 4, 8, 16, etc. If a number is entered which is not a power of two, it will be rounded to the next highest power of two. Note: A zeroll of 1 will leave the data unchanged. The Zeroll operator takes one argument. When Zeroll is selected in the processing list, the input box below the processing list will contain the argument (see Figure 5-10). To change the value of zeroll: 1. Place the mouse in the input box. The mouse pointer will change to a text cursor. 2. Using the Backspace key, delete the entry and type a new argument.
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Example: Begin with an empty processing list as shown in Figure 5-8.
Figure 5-8. Empty Process List Using the mouse button, select PreTransform and then drag down to DC Balance and release. DC Balance will appear in the processing list as shown in Figure 5-9.
Figure 5-9. Process List after Adding DC balance Again using the mouse, select PreTransform and then Zeroll. Zeroll will be entered in the processing list after DC_Balance, and the default number of times will be displayed in the input box. Change the number from 1 to 2. The processing list should now look like Figure 5-10.
Figure 5-10. Process List after Adding DC Balance and Zerolling
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Window Functions Window or apodization functions are used to enhance or to emphasize features in the data. The most common is the single exponential window function (Single Exponential). Another common apodization window is the Sinebell. The Sinebell apodization window is available in several variations. Single Exponential Single Exponential applies a single exponential with a user-adjustable broadening factor. The line-broadening factor is adjusted to approximate the decay of the FID. Line broadening has units of Hz. Use the input box to modify the broadening factor. Example: Select Window on the Menu Bar and drag the mouse to Single Exponential. Release the mouse button and sexp will appear next to the end of the processing list. Change the broadening factor by editing the input box. The process list should now look like Figure 5-11. To process the FID with the new entries in the processing list, click on .
Figure 5-11. Process list after adding Window function Transform Functions Transform functions are used to convert data from one type of domain to another. In this manual, only the Fast Fourier Transform (FFT) and Maximum Entropy will be discussed. Please consult the Delta Users Reference Guide for a discussion of other Transform menu functions (page 7-19).
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Fast Fourier Transform (FFT) Applies a Fourier transform to the input data, converting it from a free induction decay (FID) in the time domain (units in seconds) to a spectrum in the frequency domain (units in Hertz or PPM). FFT has an optional parameter that is the multiplier for the first data point of the data prior to the transform. This feature may be used to correct for baseline distortion due to incorrect sampling of the data. The multiplier is normally set to 1. Example: Select the FFT option from the Transform menu with the mouse. The FFT will be entered in the processing list as shown in Figure 5-12. Click the Process button to apply the FFT to the data and display the result in the lower window.
Figure 5-12. Process list after adding Fast Fourier Transform Notes on Maximum Entropy Maximum Entropy attempts to use the maximum entropy principle in order to reconstruct a spectrum. The entropy used to regularize the spectrum is the entropy function derived independently by Daniel and Hore (JMR 84, 1989) and Hoch and Stern (JMR 86, 1990):
M () M () M ( ) 2 1 / 2 - asinh ---------------- 1 ------------------S 1 = --------------- b b -b2
2
This entropy functional can be demonstrated to be appropriate for the regularization of MR spectra of spin 1/2 particles. b is a normalization constant that strictly should be set for the integral over all space of the number of spins with a particular shift and orientation in the sample. In general, setting b to a small value is appropriate. Two other optional parameters to Maximum Entropy are Times, the number of points in the reconstructed spectrum divided by the number of data points collected; and Noise, an estimate of the noise value of the data. The spectrum is then reconstructed by determining M which minimizes S - C (where C is the chi squared value of the reconstructed spectrum with respect to the original spectrum).
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Cursor Tool
Since PostTransform and Display menu functions require using the Cursor Tool, discussion of these menus will follow that tools introduction.
CURSOR TOOL
Because of the wide array of operations used to manipulate data geometries, a special cursor tool was developed to perform data operations. Here, we will discuss only basic usage of this tool (its operations are spelled out in more detail in the (Delta Users Reference: Mouse Cursor Tool on page 4-1)). The example here is based on data loaded in a Data Slate (accessed by selecting the button on the Delta Console). Note: The new cursor buttons replace the older cursor tool which had its own separate window. Located in the upper right of the active data geometry window, the cursor tool (illustrated below) is created automatically whenever a geometry, with data, is opened. If you are working with more than one geometry open, the cursor tool will move from window to window as you reposition your cursor. The Cursor Tool is created whenever a geometry with data is opened if the line CURSOR_TOOL_ON = TRUE appears in your .delta_configure le or if the Cursor Tool is toggled ON in the Preferences Tool. This is the default setting. 1D Zoom mode operations
Figure 5-13. 1D Zoom mode operations
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Tab Operations Key Commands Keyboard
Mode
To use the Mouse Cursor Tool, select: 1. The loaded 1D data geometry you want to work with. Note: to load a data le, use one of the File - Open menus.
2. The Tab in the upper right hand corner of the data geometry to open or close the Mouse Cursor Tool. 3. The cursor Mode (by name) that you want to use on the data. To change modes, click on the mode name. Note: You can also use function keys to change modes.
4. An operation from the picture buttons. These operations -- detailed in the Delta Users Reference: Cursor Operations on page 4-4 -- may differ according to the geometry type. 5. Select for a list of Keyboard commands. These keyboard commands vary with the cursor mode, and with the data view (at, stack, spatial). A list of these keyboard commands can be found in the Delta Users Reference: Keystrokes and Keyboard Commands on page 4-35. You can use these commands in analyzing geometries -- in integration, j-coupling, normalizing, creating peaks, changing a les reference, zooming, and sequence analysis. Some of the more commonly used techniques are elucidated in this chapter. When the geometry window is quite small, only the current operation may be visible. In this case, other operations are listed in a pull-down menu under the mode button. Other modes/keys can be selected from the popup menu accessible from the right mouse button. Note: Select spacebar to move right through the list of operations; shiftspacebar to move left through the list. In some instances, no mode button appears: Note: When, as in the Presentation Manager, the Cursor Tool Tab button is not visible: - change cursor modes using the function buttons (F1 to F12). - use the spacebar to move to the next cursor operation. - use shift - spacebar to move to the previous operation.
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Cursor Tool
Note: The mouse cursor tool is customizable in the Preferences Tool. This is true for every operation and for every mode. To change display attributes for a display area using the accelerator key functions, you must have the Input Focus in that display area.
Figure 5-14. Sample Key command menu 6. Additional functions are available using a few familiar keystrokes: The cursor mode or operation can be readily identied with a help label by selecting the right mouse button. An identier label also appears in the lower ruler of the data geometry. To select the closely related operation specied in the help label: Select ALT (or the middle mouse button). To reset this ALT operation to another related operation: Select SHIFT-CNTRL-ALT, then select another operation button (e.g. move cursor instead of delete cursor -- you will see the help change accordingly). To reset this function: Repeat the SHIFT-CNTRL-ALT combination, and select the original operation button. To zoom in any cursor mode: Hold down the SHIFT key. Select CNTRL (or right mouse) to access the popup menu from which you can select the Level Tool, autopositioning, etc.
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CURSOR MODES
The Cursor Tool can be used in various modes (discussed briey in the table below) to perform operations on geometries. Each mode in turn has a number of operations (described in the Delta Users Reference: Mouse Cursor Tool on page 4-1.) The Data Slate is invoked here to illustrate cursor operations. It is described in its online help.
Select Zoom (F1) Select (F2) Region (F3) To zoom in on a portion of the le by holding down the mouse button and dragging over the area you wish to zoom. To select the le as the current geometry by clicking on it. To draw regions and obtain the coordinates of an area of the geometry. White index marks showing the boundary of the region will be displayed on the axis (Both axes for 2D). The region can be moved freely in the display area. To use cursors to see the coordinates of a particular point in the data le. Note: if data areas are connected, manipulating a cursor in one area will affect the cursor in a connected area. Reference (F5) Peak (F6) Pick (F7) Integral (F8) Text (F9) PiP (F10) To set a chemical shift reference point. To manipulate peaks and integrals, and to set their noise and threshold levels. To measure x and y coordinates. To perform integration, set slope, offset and length for integrals, and to manually integrate areas. To annotate the le. To create and frame a selected part of the geometry within the present one. This picture within a picture is linked to the original geometry. To offset the data display in data overlay. To import standard molecule les (*.mol) into a Delta data le to display a molecular representation of the data with the spectrum in the geometry widget. This mode (in conjunction with add-select peak operations) lets you select atoms within molecules and link them to peaks.
Cursor (F4)
Offset (F11) Molecule (F12)
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Cursor Modes
Zoom, Region, PiP -- a Sampler Three modes -- Zoom, Region, and Pip -- allow you to isolate a segment of the data for closer study. Zoom Use zoom operations to isolate a segment of a region for closer study. To zoom in on the data: Select Zoom mode in the Mouse Cursor Tool:
Select
. Then draw a box around the area which you want to see ll the screen.
Figure 5-15. Sample Zoom Operation Note: This zoom button in the mouse cursor tool also works in 1D and nD Processors.
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Region Use region operations to create, move, resize or delete a geometry region. To create a region:
Select and draw the region. White index marks showing the boundary of the region will be displayed on the axes. The region can be moved freely in the display area. Note: When the mouse button is released, the associated Data Slate will be updated. When you delete a region, the associated Data Slate window will be closed. When you create a region on a data slate, a virtual geometry of this region pops up on the adjoining data slate. These two regions are connected by default. An operation performed on one appears on the other (e.g., if you create a cursor, it appears in the other geometry; if you zoom in on the data, the other geometry reects this zoom.)
Figure 5-16. Sample Region Operation
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Cursor Modes
PiP PiP allows you to create a virtual sub-geometry, an independent child with the same data as the parent geometry in which you can show or print expansion (for example). To create a PiP: With the Pip mode on the cursor tool selected, select: to zoom in on and frame a part of the geometry. (or Prettify in the left of the selected geometry. menu, or type p to moves the PiP to the upper
Figure 5-17. Sample PiP Operation
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MENUS FOR EXTENDED 1D PROCESSING

This section discusses PostTransform (page 5-26) and Display (page 5-33) functions. Post Transform Functions
PostTransform functions are data analysis and reduction functions applied after an FFT. Only phasing and baseline correction will be discussed here. The Delta Users Reference Guide lists all of these functions (page 7-24).
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PO
P1
PP Figure 5-18. Spectrum before Phase Correction. To phase a spectrum manually: Use the P0 and P1 buttons in the lower right-hand corner. The data in the output window will immediately reflect the phase change. 1. Adjust P0 by clicking the appropriate button. Each click will increase the value of P0 by the value on the button. (See Figure 5-19.) Use P0 to phase the area around the pivot point (PP). 2. Adjust P1 by clicking the appropriate button. Each click will increase the value of P1 by the value on the button. (See Figure 5-20.) The P1 correction will have the greatest effect farthest away from PP. To get a better look at the data peaks and baseline, and to make the phasing easier, use the Zoom cursor to expand the spectrum, vertically and horizontally. Zooming may be done at any time without affecting the phasing. To unzoom the data: use the Backspace key, or the Home key.
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Figure 5-19. Phase Correction Performed Using P0
Figure 5-20. Further Phase Correction Using P1
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Selecting the Phasing Pivot Point (PP) Some data may be phased more easily by moving the phasing pivot point (PP). The PP point is the data point that is not affected by the P1 phase correction. It is shown by the yellow tick mark on the x-axis. The value of PP is displayed in the box located below the P1 buttons. To change the PP: 1. Select the Pick mode on the Cursor Tool (CTool) or F7. 2. Select , then click the Pick cursor on the data at the new PP location.
Storing the Phase Correction When the spectrum is satisfactorily phased, the newly adjusted phase correction must be inserted into the processing list because the interactive phase correction is applied solely to the visual display (to improve display response). To apply the phase correction to the data: Select the Apply Phase option under the PostTransform - Phase submenu, then process the data. You can also click the Apply button. The values from the P0 and PP input boxes will be transferred to the processing list. Be sure to select the Process button to apply the phase information to the data set.
Figure 5-21. Applying the Phase Correction
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Automatic Phasing The data system can also calculate approximate phase corrections for you. Invoke Autophase in one of these two ways: 1. Select from the 1D Processor icon bar to calculate the autophase correction and place the results in the P0 and P1 boxes. You may touch up these autophase corrections, but you must always apply the values using the Automatic Phase command under the PostTransform menu. Note: Automatic Phase can also be run by selecting that command in the PostTransform - Phase menu. 2. Or, select the Automatic MachinePhase option under the PostTransform - Phase menu. MachinePhase will be inserted into the processing list and will be executed each time the processing list is applied to the data. Machine Phase autophases the spectrum using the experimental and machine parameters: pulse width (X90), dead time, pre-acquisition delay, lter type and lter width. If these required parameters are not present (as in the case of older les) it defaults to the same algorithm as the one-dimensional Automatic Phase. Only the current major axis is phased. Interactive Baseline Correction After phasing, NMR data may have an baseline that is uneven. If the Baseline Correction - Base Correct automatic processing command under the PostTransform menu does not completely correct the baseline, you can use the Interactive Baseline Correction, Base Correct (Interactive). A separate interactive iBase_Correct window will appear during processing (Figure 5-22). The Interactive Baseline Correction allows you to apply a polynomial (up to 5th order) correction, a piece wise linear correction, or a trigonometric function correction.
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a)
b)
Figure 5-22. Interactive Baseline Correction - a) Polynomial and b) Piece wise Linear You can position up to 32 points in the data to t any of these functions. Select: to create a new data point marker which will be displayed as a crosshair. Create a second cursor with the mouse.
to delete a data point marker.
to move the closest data point marker to a different position in the data set. If more than 32 points are required to correct the baseline, correction can be applied successive times. In this case, select the number of neighboring data points averaged (Ave Pnts:), and turn on or off the automatic selection of the End_Points. Preview the t on the display (Figure 5-23) by using the Preview button before the data is changed (the Accept button). A dual display mode can be enabled by using the Show Curve button (Figure 5-22).
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Figure 5-23. Interactive Baseline Correction Preview
Figure 5-24. Interactive Baseline Correction with Show Curve Enabled
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Display Functions Various display functions in 1D processing are discussed below.
Axial Units The NMR spectrum axis may be displayed in several different units. Immediately after the FFT, the units will be Hertz. The units may be converted to parts per million either by inserting the PPM command in the processing list (Figure 5-25) or by changing the ruler axis to PPM under the Rulers menu. The PPM command changes the base unit of the data file. This differs from the Ruler change, which is a temporary change for that window only. The next time the data file is opened, the units will revert to the base file units.
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Figure 5-25. Process list after converting data axis to PPM Referencing Referencing the NMR spectrum allows you to mark the chemical shift axis relative to a known value. For NMR data collected on an Eclipse spectrometer, the data will be automatically referenced by the spectrometer. For other JEOL NMR data such as GSX or EX, select Automatic Reference under the Display menu of the 1D processor. For non-JEOL NMR data, you must use the Reference option in the Display menu, or the Reference Tool under the Delta Console. Referencing Eclipse NMR Data NMR data from an Eclipse NMR spectrometer will already be referenced based on an absolute frequency from the gamma.def and solvent.def file. If the reference needs to be adjusted, use either the Reference command in the Display menu or the Reference Tool. You can also use the Reference - Unreference setting. Reference Tool The Reference Tool (Figure 5-26) is located under the Tools menu in the Delta Console.
Figure 5-26. Reference Tool
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To set reference registers: 1. Open the Reference Tool from the Tools - Geometry Tools menu of the Delta Console. 2. Select the Reference mode from the Cursor Tool.
3. Select . Then click on a spot in the geometry. The current reference coordinates will be displayed in the Reference Tool. They can be rounded off to the nearest whole number by selecting Round in the key menu or by pressing R on the keyboard. Reference Command The Reference option in the Display menu of the 1D processor assigns a reference point to any location in the data using a processing list. The Reference function takes two values: the position in the data and the new reference value. These values are entered into the boxes below the processing list as shown in Figure 5-27. Click the Process button to execute the processing list. Automatic Reference Command If the NMR data was imported from a JEOL GSX, or EX spectrometer, the Automatic Reference command will calculate the 0 PPM reference position and apply it to the data. This calculation is valid only for H and C data.
Figure 5-27. Reference in Processing List To enter position and reference values in this processing list:
Select , then Type in the reference value. Process the data le.
to indicate the peak position.
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Note: The position buffer above accepts [ppm] units.
Copy Reference Tool
Figure 5-28. Copy Reference Tool This tool (Figure 5-28) lets you nger data to copy references from a Source File to a Target File (using the Source and Target buttons), then perform referencing on one to all dimensions of the target le. It is more fully described in the on-line help and the Delta Users Reference: Copy Reference Tool on page 20-1. To invoke the Copy Reference tool: Under the Tools menu in the Delta console, select Geometry Tools, then Ext. Reference. Or, you may use the Reference - Copy Reference command in the Display menu. Save Command Select the Save command in the Display menu to write out a data le in the processing list, specifying a lename to save the data to. If the lename is not specied, then the le will be saved with the same name, but with an incremented version number. Peak Picking and Integration To adjust the peak threshold: 1. To display the threshold, turn on Statistics (ALT T) in the Options menu of the popup menu displayed when the right mouse button is pressed down when you are in a data geometry. In the resulting data geometry, the green line indicates the positive peak threshold; the red, the negative peak threshold; and the gray, the noise threshold (page 5-42). 2. Place the mouse in the Peak mode from the Cursor Tool (F6).
3. Select , then drag the mouse cursor to adjust the peak threshold. 4. After moving the threshold, select one of the Peak Pick & Integration icons to
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execute another peak pick at the new level.
5. You also use the Peak Pick/Integrate command in the Display menu to calculate peaks and/or integrals for the data set over a particular range. The select enumeration box allows you to specify Peaks, Integrals, or Both. To delete a peak or group of peaks: 1. Select Peak mode in the Mouse Cursor Tool.
1. Select . 2. Click and drag the mouse on or across the peaks you wish to delete. The peaks should turn yellow to indicate that they are selected. 3. Press the keyboard letter d to delete them.
4. Or, select
to delete the selected peak.
To create an integral: 1. Select Integral mode in the Mouse Cursor Tool. 2. Select . Place the cursor at the desired location and diagonally holding the
mouse button in the gray portion just below the x ruler. Drag to create the integral. To normalize an integral: 1. Select Integral mode in the Mouse Cursor Tool. 2. Select . Then click on the desired integral. The integral will turn yellow when
selected. 3. Select Set Integral Normal from the Options menu of the 1D processor. 4. Enter the desired normalization constant. All of the integrals will immediately normalize to the selected integral. To delete an integral: 1. Select Integral mode in the Mouse Cursor Tool. 2. Click on the desired integral. The integral will turn yellow when selected.
3. Select
to delete the selected integral.
To link peaks to atoms: 1. Select Molecule mode in the Mouse Cursor Tool.
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1. Select a peak (using ) and an atom (using ). 2. Press the key corresponding to the dimension you would like to hook them up to: X, Y, Z, A, B, C, D, E. Up to three peaks can be connected to a single atom, however, any number of atoms can be connected to the same peak. If an atom has already been connected to at least one peak, you may still connect it to more peaks but you must do this with the Spread Sheet tool. The following example uses the X dimension; but all dimensions work the same way. When you connect a peak to an atom for the rst time, two things happen: 1. The Spin X parameter gets set and Seqn X gets set (where n is 1, 2, or 3). 2. The value placed in Spin X is equal to 65536 minus the molecule window number. Thus, for molecule window 2, 65534 will be placed in Spin X. Seqn X gets assigned the atom number to which the peak got connected in the order 1, 2, then 3. 3. Knowing this, you can see now that a single peak cannot be connected to atoms from different molecule windows, but a peak can be connected to up to three atoms from the same molecule window.
Figure 5-29. Spreadsheet Tool To unlink a peak from an atom: 1. Select the atom you wish to detach. 2. Then hold down the SHIFT key and press the key corresponding to the dimension you wish to unhook the peak from. 3. Press the T key to deselect all atoms in the selected molecule window except those that are connected to peaks. If a molecule window is not selected, then the atoms in
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window one will be deselected if it exists. You don't necessarily need to use the mouse to connect peaks to atoms. You could do the entire process in the Spread Sheet Tool (see Figure 5-29 on page 5-38.) To calculate a J coupling constant between two peaks: 1. Peak pick the data. 2. Select Peak mode in the Mouse Cursor Tool.
3. Select . 4. Click on two peaks with the mouse button. They should turn yellow when selected. 5. Press the keyboard letter j to calculate and display the J constant. The coupling constant is simply the frequency difference between the peaks. In the case of strong coupling or second order spectra the value is not the true coupling constant. Peak Picking and Data Reduction Peak picking can be done either interactively using the Peak Pick & Integration icon, or by including the Peak Pick/Integrate function from the Display menu in the processing list. The display of the peak data and integration are controlled independently by selecting Auto Peak Pick or Auto Integrate in the Display menu. All of the peak pick entries are also stored in the Spread Sheet. To view the peak listing on the screen: The Peak Pick viewing Option must be activated. Select Peak Pick in the data geometry popup Options menu (page 5-60) which you can select using the right mouse button when positioned in the data geometry, or use the ALT-P accelerator key. TO VIEW INTEGRALS ON THE SCREEN: Activate the Integrals viewing option by selecting Integrals in the geometry popup options menu; or use the ALT-I accelerator key.
Automatic Peak Picking To auto peak pick the spectrum:
Select
on the 1D Processor Tool menu bar.
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green line
Figure 5-30. 1D Processor with auto-peakpicked 1H data If a greater than desirable number of peaks are picked, select Peak mode from the cursor tool (F6)
Then, select to adjust the peak threshold. Select the green threshold line and move it up to include only the desired peaks. If you cannot see the green peak threshold line, use Alt T to turn on statistics (or select Statistics in the Options menu that appears when you press the right cursor button when in the data geometry).
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green line
Figure 5-31. 1D Processor with adjusted peak threshold Then, select again. The data will now be auto peak-picked again.
Note: Both automatic Peak Picking and Integration are performed by the same function, although the display of the peak data and integration are controlled independently. Integration is done either interactively using the Peak Pick & Integration icon, or by including the Peak Pick/Integrate function from the Display menu in the processing list. All integration values are stored in the Spreadsheet.
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Pick Tool Use the Pick Tool to pick a geometry with precision.
Figure 5-32. Pick Tool To invoke this tool: Select the Pick Tool command found under Geometry Tools in the Tools menu of the Delta Console. Use the Select File button to select the le whose picks you want to control, and nger its geometry. When the geometry is selected, the maximum values for each ruler are loaded into the constrained input boxes. This tool is more fully described in the help le (page 44-1). Noise Level and Threshold To view the noise level and threshold: Perform a zoom on a selected portion of the baseline of the data geometry, until you clearly see the noise. Turn on Statistics (ALT-T) in the popup geometry Options menu. Statistics will show on the 1D display as three lines: positive threshold, noise level, and negative threshold (see Figure 5-33).
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Positive peak threshold Noise threshold
Negative peak threshold
Figure 5-33. Peak Pick Threshold Display Note: The Home key on your keyboard will take you back to the original view of the data. The End key makes the top peak move to the top of the screen. To adjust the threshold and noise level: Select Peak mode in the Cursor Tool. Then use the following Cursor tool options to adjust the zero line, threshold, and noise levels. After the new threshold and noise level is set, click the Peak Pick & Integration icon to execute a new peak pick.
Select: To set the peak threshold (green and red lines). The positive and negative thresholds are coupled and move symmetrically about the zero line.
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Select: To set a noise threshold level (gray line) to screen out the noise for better peak selection.
To adjust the baseplane of the data display (white line).
To manually pick peaks: Peaks may be added or removed manually using Peak mode on the Cursor Tool. To add a peak: 1. Turn on peak viewing with Peak Pick (ALT-P) in the data geometry popup options menu. If the Peak Above option (ALT-U) is not on, the lower display area will shrink to make room for the peak value display. 2. Put the Mouse Cursor Tool in Peak mode.
3. Select . 4. Click on the spot where you wish the peak to appear. If the peak does not exceed the current threshold and noise level, a message window will appear. Adjust the threshold and noise level as described above to add a small peak. To force create a peak: 1. Put the cursor in Peak mode.
2. Select . This creates a peak pick whether or not that data position meets normal peak criteria. To select a single peak: 1. Put the cursor in Peak mode. 2. Select .
3. Click on the peak position with the mouse button. The selected peak will have a small yellow marker. To select an additional peak: Select .
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To select a whole range of peaks: Click the mouse button and drag across the desired peaks, then release. The selected peak values will be displayed in the cursor color. To select all peaks in a data set: Put the cursor in Peak mode, and press the keyboard letter a. To remove a single peak from a data set:
Select
To remove a group or range of peaks: Select the peaks with a click and drag with the mouse button. Press the d key to delete the selected peaks. To remove all the peaks: Select all the peaks by pressing a, then delete the peaks by pressing d on the keyboard. To display peaks: The Peak listing will normally be displayed underneath the peaks (default) as shown in Figure 5-34. The Peak listing may be displayed above the peaks (Figure 5-35) by selecting Peak Above in the data geometry popup options menu, or ALT-U.
Figure 5-34. Peak Display (default)
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Figure 5-35. Peak Display with Peaks Above Option Enabled Coupling Constants Coupling Constants are a special class of the peak display type. When two peaks are selected, the difference between the peaks in Hz will be calculated by typing the letter j on the keyboard (Figure 5-36). The coupling constant value will also be entered into the Spreadsheet. The calculated coupling constant is simply the frequency difference between the peaks. In the case of strong coupling or second order spectra the value is not the true coupling constant.
Figure 5-36. Peak Display with J Coupling Constants Integrals
Use integral operations to set slope, offset and length for integrals, and to manually integrate areas of a geometry. For more detail on all Integral functions, consult page 4-21.
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Manual Integration Integrals may be added or removed manually using the Integral mode on the Cursor Tool. These operations let you set slope, offset and length for integrals, and manually integrate areas of a geometry. To add an integral: 1. To activate Integral viewing, select Integrals (ALT-I) in the geometry popup options menu. 2. Then, select Integral mode in the Cursor Tool (F8).
With the create integral button selected, place the mouse in the ruled area of the X scale at the place where you want to begin integration, and drag it to where you want the integration to end. You can repeat this procedure for all areas of interest.
Figure 5-37. 1D processor with data peaks integrated When an integral region is created, the slope for that integral will be computed automatically. The software uses the average of 10 data points at each end of the integral region to calculate the slope correction.
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To select a single integral:
Select
, and select an integral. Note that the selected integral turns yellow.
To normalize a selected integral: Select Options - Set Integral Normal in the menu bar of the 1D Processor. The Integral Normal Value window comes up.
Assign a value by typing it into the box provided. (for example, type 3 for a peak that has three protons). Then click Enter. All integrals will be scaled according to that peak. To select multiple integrals: Press the SHIFT key and click the mouse button on each additional integral.
Use to select a group or range of integrals: Click the mouse button and drag across the desired integrals, then release the button. The selected integrals will be displayed in yellow. To select all the integrals in a data set: Select the Integration cursor mode, place the cursor in the data window, and press a on the keyboard. All the integrals will change color. Integral Slope Adjustment Each integral may be adjusted individually for slope (Figure 5-38). When an integral is selected (yellow), a blue line is displayed below the integral. This line represents the correction function applied to that selected integral.
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Figure 5-38. Integral Slope Adjustment To adjust the slope of an integral: 1. Change the cursor to Integral mode. 2. Select while using the mouse to grab either end (the small box) of the blue line at the base of the integral. The slope adjustment is an up/down mouse motion. The middle mouse button will allow adjustment of the integral region length, in addition to the slope. To remove an integral from a data set: Select it, and then use . Press the SHIFT key and click on the integral with the middle mouse button. To delete a group or range of integrals: Select the integrals as above and type d. To change the vertical gain of an integral or group of integrals:
Select the integral and type g. The integral will be expanded vertically to fill the screen. The vertical gains of the data and integrals are independent; therefore, the data may be expanded and plotted without affecting the integral gain scaling. To plot Integral Expansion: Plotting Integral Expansion allows you to view up to 12 different integrals more closely, plotting from 2 to 9 integrals on a single page. The plot lets you see each peak with its integral. Select Options - Plot Integral Expansion. This window comes up.
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Fill in the number of integrals you would like to see. The Y-scaling value, on by default, ts the y dimension to the plot box. Then select Plot to plot this data. 4.3.6 Plotting the Spectrum
To plot the spectrum, click on
in the tool bar.
Transfer Integral Tool The Transfer Integral Tool (Figure 5-39) can be used to create, store, and retrieve integration templates. The integral templates may be applied directly to data in other windows, or saved to disk for retrieval at a later time. An integration template consists of a list of integral and normalization regions. Normalized integrals are indicated by an N following the integral region in the template list.
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Figure 5-39. Transfer Integral Tool To use the Transfer Integral tool: Select Tools-Geometry Tools-Transfer Integral Tool from the Delta Console. Select the Apply Integral command under the Display menu of the 1D Processor to include the integration templates in a processing list. For more information on the Transfer Integral tool, see the Delta Users Reference: Transfer Integral Tool on page 60-1. Peak Deconvolution Overlapping NMR peaks may be deconvolved to determine peak ratios. After a peak is deconvolved, the information for that peak is automatically updated in the Spreadsheet (Figure 5-49). The deconvolution routine uses the peak positions from the Peak Pick information. All the peaks in the display window to be deconvolved must have peak pick positions.
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Figure 5-40. Data before Deconvolution .
Figure 5-41. Deconvolved Data
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To deconvolve a peak or group of peaks: 1. Peak Pick the data set and expand the desired area as in Figure 5-40. The deconvolution will occur to all peaks in the display window. If the entire data set is displayed, the entire data set will be deconvolved (this may take a long time). 2. Select Deconvolve (ALT K) in the Options popup menu accessible from the data geometry window. This option enables the deconvolution display. 3. Select the Peak mode from the Cursor Tool (F6). 4. Select the peaks to be deconvolved. 5. From the Key menu, with the mouse button, select Fit Lorentzian, Fit Gaussian, or Fit Mixed. Or, press the keyboard letters l for Lorentzian, f for Gaussian, or x for Mixed. Deconvolution will begin immediately. 6. Deconvolution is an iterative procedure. A chi-square value of the t is displayed in the Delta Console window. Results are only displayed if show_deconvolution_results is true in the Preferences Tool. 7. Repeat the t until a consistent value is obtained. The deconvolved peaks are displayed in yellow. The difference between the deconvolved peaks and the spectrum is displayed in red above the data (Figure 5-41). 8. The sum of the deconvolved peaks can be displayed (Figure 5-42) by using Deconvolve Sum (ALT H) in the geometry popup menu in the Menu bar. For example, if you select a group of peaks, then turn on Deconvolve and Deconvolve Sum, the green line represents the data, with its peaks. the yellow line shows a mathematical model of each peak, called a deconvolution. the red line above shows the difference between the actual peak and the theoretical model -- the deconvolve sum. 9. Deconvolve Unsel will show the deconvolutions of all peaks whether selected or not (Figure 5-43). 10. Often it is necessary to add additional peaks. This may be done at any time by using the create peak option with the CTRL - middle mouse button feature. 11. Finally, after deconvolution, with the deconvolve bit set to TRUE, data will be updated for the deconvolved peaks.
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Figure 5-42. Deconvolved Data with Deconvolve Sum
Figure 5-43. Deconvolved Data with Deconvolve Unsel
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Figure 5-44. Spreadsheet after a Deconvolution Annotation DELTA supports on-screen annotation, which is created with the Text mode (F9) from the Cursor Tool. The data set must be saved after the annotations are created. The annotations are stored with the data. The annotation display is controlled by the Annotation options (ALT A) under the data geometry popup options menu. To create an annotation: 1. Locate and expand the peak of interest. 2. Place the mouse pointer in the Text mode.
3. Select . The cursor will change to an I-beam insertion marker. 4. Select the desired location with the marker, and press the mouse button. 5. Type the text. Greek characters are accessible using the ALT key. Annotations are limited to a single line of text. 6. Type Enter to terminate the annotation input mode. Note: When an annotation is selected (yellow), all other annotations will disappear from the screen until the selected annotation is terminated or deselected. To edit an existing annotation: 1. Place the mouse pointer in Text mode.
2. Select . 3. Select the annotation you want to edit. It will turn yellow. Use the arrow keys to move the I-beam insertion point to edit the string. 4. Type Enter to terminate the editing mode.
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To delete an annotation:
1. Select 2. Then click on the annotation you want to remove. To rotate an annotation: 1. Place the mouse pointer in Text mode.
2. Select . 3. Select the annotation; it will turn yellow. 4. Press the Page Up keyboard key to rotate 90 right (up) or Page Down keyboard key to rotate -90 left (down). Annotations may be rotated and shifted (anchored) about the insertion point. Rotation and shifts may be done at any time in any order. To shift an annotation: 1. Place the mouse pointer in Text mode.
2. Select . 3. Select the annotation; it will turn yellow. 4. Press the Home keyboard key to shift the annotation to the right, or the End keyboard key to shift it to the left.
SHIFT RIGHT SHIFT LEFT
ROTATE 90 ROTATE -90
Figure 5-45. Annotation Rotation & Shift Keys Greek characters can be generated by holding the left ALT key and typing in the appropriate key (a= alpha, b = beta, etc.) To change the font/attributes/size of annotations: 1. Place the mouse pointer in Text mode.
2. Select . 3. Then select the annotation. 4. Then use the mouse cursor to bring up a selection menu.
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Use these key combinations: Select: Shift - arrow key to change the font. Ctrl - arrow key to change the font size. Alt - arrow key to change the font attribute.
Figure 5-46. Data after Annotation Molecules Use Molecule mode in the Mouse Cursor Tool to import standard molecule les (*.mol) into a Delta data le to display a molecular representation of the data with the spectrum in the geometry widget. Each molecule is made up of atoms and bonds. An atom is located at the both ends of each bond. Any number of these atoms can be selected or deselected, then hooked up to peaks in the data le using Add-Select Peak and Deselect Peak operations. Note: Before you can add molecules to display in Delta, you must rst have a .mol le that is in standard molecule le format. Delta does not yet provide any mechanism for creating these types of les, so you must create one by using another software package. It is assumed that a.mol le exists for Delta to import.
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To import a molecule interactively: Select:
To create a molecule window. ALT: To move a molecule window.
To move a molecule window. ALT: To resize a molecule window.
To resize a molecule window. ALT: To move a molecule window.
To select or deselect a molecule window. Only one molecule window can be selected at a time per data le. ALT: To resize a molecule window. To delete a molecule window. This will not remove the molecule information from the data le, it only removes the window in which it is displayed. ALT: To resize a molecule window. To select an atom. Click on the atom you wish to select or deselect. Then connect atoms to peaks in the data le, using the Add-Select Peak and Deselect Peak operations below. ALT: To select peaks. To select peaks (used to connect a selected atom with a peak in the data le). ALT: To delete peaks.
To unselect peaks. ALT: To select peaks.
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Data Window Manipulations: Level Tool
First, open a data le in a data geometry window. Any data le can have a molecule imported into it, but only 1D and at 2D geometries will be able to display the molecules.
In molecule mode, select
and click and drag a window on top of the
spectrum in the geometry. A pop-up box will then appear prompting you to select a .mol le to display in the window. Select the le to be drawn in the window.
DATA WINDOW MANIPULATIONS: LEVEL TOOL
Contours (I)
Colors (II)
Figure 5-47. Level Tool -- Contour View (I) and Colors View (II) The Level Tool can be used whenever there is a data (geometry) display window on the screen. Its effects are applied only to the currently active (selected) geometry.
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Although the main purpose of the Level Tool is for 2D contouring, it also provides a mechanism for changing the colors of the contour levels and how they are drawn. You can also use the Level Tool to turn on and off the positive and negative data. This tool is described in the online help -- Delta Users Reference Guide, page 5-1. To invoke the Level Tool: Move the mouse inside the geometry. Hold down the right mouse button, select Tool Congure then Level Tool. The contour view (I, above) will display. This tool also comes up by default when you have set the Level Tool button in the Geometry Page of the Preference Tool. Use the right mouse button to toggle between the two Level Tool displays.
DATA WINDOW MANIPULATIONS: GEOMETRY OPTIONS MENU

Use the Options menu to perform the following operations on the data geometry:
To use these geometry options: with the right mouse button pressed, select Options in the popup menu, then select: All overlays [Alt O] Annotations [Alt A] Atom Numbers [Sh-AltA] Atom Select Numbers [Sh-Alt-S] Atom Sequence [Sh-AltQ] Comment [Shift Alt C] Cursors [Alt C] Data [Alt D] To display the lename of all the overlays not just the current one (the lenames option must also be toggled on). To display text annotations added to the le. To represent the atom number as set in the .mol le. Atom numbers are displayed in the molecule on each atom. Only numbers will be visible when the atom is selected. To see the atom numbers appear above the peaks to which they are connected. Sequence must be on (Alt-J). To turn on the le comment. To show the cursors. To show the data.
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Data Window Manipulations: Geometry Options Menu
To use these geometry options: with the right mouse button pressed, select Options in the popup menu, then select: To show data points (this marking is visible as you zoom in closely on the data).
Datapoints [Alt N]
Figure 5-48. Zoomed view of data showing Data points Deconvolve [Alt K] To show the deconvolutions of selected peaks. Used for 1D only. See page 3-5.
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To use these geometry options: with the right mouse button pressed, select Options in the popup menu, then select:
Deconvolve Sum
Deconvolve Sum [Alt H]
To show the sum of all the displayed deconvolutions.
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Data Window Manipulations: Geometry Options Menu
To use these geometry options: with the right mouse button pressed, select Options in the popup menu, then select: To show the deconvolutions of all peaks whether selected or not. Used for 1D only.
Deconvolve Unsel [ShAlt-K]
File Name [Alt F] Geom Zooms [Alt W] Grid [Alt G] Integrals [Alt I] Integral value [Alt Q] Line Hiding [Alt L] Molecules [Sh-Alt-M] Molecule Border [ShAlt-D] Molecule Titles [Sh-AltT] Negative Levels [Sh-AltN] Peak above [Alt U] Peak Integration [Alt E]
To show the lename of the le. To put a blue box around the area selected for a PiP. To show the grid on the data geometry. To display integrals. To display the numerical value of each integral. To hide lines in stack plots. To show/hide the molecule windows. To turn on/off the border around the molecule windows. To show/hide the title(s) in the molecule window. To show/hide negative nD data levels (hides them when off). To display peak position above the peaks in 1D data geometries. To display the integral value of the peaks in 1D data geometries.
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To use these geometry options: with the right mouse button pressed, select Options in the popup menu, then select: Peak picks [Alt P] Perspective [Alt V] PiP border [Alt S] Plot border [Sh-Alt B] Positive Levels [Sh-Alt P] Region [Alt R] To display the peak pick information. To turn on/off foreshortening for 3D displays. To put a blue box around PiPs. To put a box around PiPs in a printed plot. To toggle on/off the positive levels in nD data geometries. To display regions using a white box. To view the sequential sequence assignment of a spectrum, a series of connecting marks indicating sequence direction (e.g., these are especially helpful in assigning the 2D NMR spectra of Proteins.) If the le is a slice out of a higher dimensionality le, then this displays the lename of the original le and the position of the slice. To allow the cursor tool to display on the geometry. To display baseline, noise level and peak thresholds on the geometry. See (page 3-6). To display the x ruler. To display the y ruler. To display the z ruler in multidimensional les.
Sequence [Alt J]
Shadow dimensions [Alt B] Show cursor tool [Shift Alt S] Statistics [Alt T] x ruler [Alt X] y ruler [Alt Y] z ruler [Alt Z]
DATA INFORMATION DISPLAY: SPREADSHEET TOOL

The Spreadsheet Tool is used to display and print peak, integral and assignment information. To start the spreadsheet: Select on the Delta Console. A red outline of a window will appear. Position the window at a convenient location, then click and drag the mouse to enlarge the window to a convenient size (see Figure 5-49.)
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Data Information Display: Spreadsheet Tool
Loading Data into the Spread Sheet To load the Spread Sheet with a data set: Select on the Spread Sheet. Click on a data set in any window and the peak information will automatically load into the Spread Sheet. If the data set has not been Peak Picked, no information will be displayed. For more information on the Spread Sheet Tool, refer to the Delta Users Reference: Spreadsheet Tool on page 57-1.
Figure 5-49. Spreadsheet Tool Drag and Drop Drag and Drop lets you copy parameters from a data geometry to a spreadsheet, or from one spreadsheet to another.
Use the Drag and Drop Dragon to copy data from a data geometry to a spreadsheet: Select the right mouse cursor button (or Ctrl-left mouse button) while on a data geometry (or a spreadsheet) and, before the drag and drop dragon disappears, move the cursor to an empty spreadsheet (or other widget) and let go of the button. The values of the data will appear in the spreadsheet (or other widget). Use Drag and Drop to copy, from one window to another: text data parameters -- from a geometry into a spreadsheet or from one spreadsheet to another. For example, Drag and Drop lets you transfer information about peak intensity (height on the y scale) and integrals (total area covered by a peak.) colors -- in the Preferences Tool only. For a fuller description of Drag and Drop, see page 3-7 and page 57-2.
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SAVING PROCESSED DATA This section describes how to save 1D NMR data on the hard disk after data processing is complete. To save data to hard disk:
Click on the data save icon on the 1D Processor tool bar The processed data is saved. Note: The FID is automatically saved. To save data under a new lename:
1. Move the mouse pointer to File in the menu bar in the 1D Processor window. 2. Press and hold down the mouse button. A pull-down menu appears. 1. Move the mouse pointer to File in the menu bar in the 1D Processor window. 2. Press and hold down the mouse button. A pull-down menu appears.
3. Move the mouse pointer to Save As in the pull-down menu, and release the mouse button.
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Plotting Data
The Save Data File window opens: Current directory name List of Subdirectories Input le lter File version number List of les
File Type lename Figure 5-50. Save Data File Window
4. Click on
5. Specify the lename, and click on the Ok button. The le is stored on the hard disk, and the Save Data File window automatically closes. Note: The le version number does not implicitly differentiate between FID data and processed data. That is, the data of version 1 is not always FID. The le info eld will have [s] in it if it is a FID; [ppm] or [Hz] if it is a processed data set.
PLOTTING DATA
Delta supports output only in postscript (either in color or in black & white). To generate routine data plots: Select from the Delta tool you are in. Selecting this button brings up the Print Options Tool which allows you to select a data destination (printer and/or le), a printer, printer specication, paper size and orientation:
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Figure 5-51. Print Options Window Delta uses WYSIWYG (what you see is what you get) plotting. If a spectrum or option (integral, peak pick, coupling constant, etc.) is displayed in the window, it will appear in the plot. The default plot will cover the full page of the default plotter. The default plot device and plot format is specified in the .delta_configure file. Consult Appendix E for more information about the .delta_configure file. To place a standard list of parameters on a plot: Use Plot Params located under the Preference menu on the Menu bar. The default list of parameters is created by the .delta_parameter_list file in your home directory. The default plot format and parameter location is determined in the .delta_configure file. To customize plots, use the Presentation Manager. This powerful tool allows you to do far more than design the contents and composition of your printout. It is outlined below, and described more fully in online help or the Delta Users Reference: Presentation Manager on page 46-1.
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Presentation Manager
PRESENTATION MANAGER
.
Figure 5-52. Presentation Manager Use the Presentation Manager to conveniently submit data to a number of processes, and design a meaningful presentation. For example, you could start with a single data le and do any of the following: create templates, page 5-70, output the data (and/or imported text and graphics) to Presentation Manager boxes, page 5-72, take projections or views of the data, page 5-72, add parameter lists, page 5-72, organize a coherent presentation, creating links and setting limits, page 5-72, and preview and plot the presentation, page 5-76. The Presentation Manager lets you import, process and compare data taken from
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experiments run on different samples. As you become an experienced user, it will serve you as a powerful mini processor. Judicious use of this tool -- limited only by your imagination -- could even render obsolete use of other processing tools for certain data. For instance, you could use the Presentation Manager to print a 2d contour diagram, with a 1d projection: annotating, picking, labelling or ltering its peaks. To invoke the Presentation Manager:
Select from the Delta Console. Or select File, then Presentation Manager (or Tools, then Presentation Manager) from the Delta Console menu. Then from the list of les in Open Data window, make a selection and select OK. The Presentation Manager consists of: a number of menus and icons, a presentation screen you use like a blackboard to design your presentation (drawing boxes lled with data or parameter lists from geometries), a series of rules by means of which you locate your boxes on the presentation screen - boxes which can include data, data parameters, encapsulated postscript (.eps), IRIS image (.rgb) or text (.txt) les, and four select buttons to do the following: to get features from the ngered geometries to get ruler limits from the ngered geometries to disallow box movement, and to retain the ruler settings. When off, changing a box's type will erase that box's rulers.
Note: Presentation manager never retains a data source, but it does the processing, making a virtual copy of any le loaded into it.
Presentation Manager Templates

You read data into a Presentation Manager template -- one that is predened or one that you design. It is recommended that you start with predened templates. To use a predened template: 1. Select the Template menu in the Geometry menu of the Presentation Manager menu bar. 2. Select an appropriate template (e.g., cosy) 3. Select a le from the Open File window , or use to nger data from an
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open geometry.
Note: The persistent rulers button on the Presentation Manager must be selected, in order to nger data into Presentation Manager. 4. If the geometry you select is a zoom view, use 5. Use to load the data parameters instead. to select the whole le.
The second option - redening a template (then renaming and saving it) - lets you add to your collection of predened templates. In this manner you could add a processing list to a selected Presentation Manager box. 1. 2. 3. 4. To redene a template: Select a predened template from the selection in the Template menu under Geometry. Follow the instructions below to alter: the presentation structure (moving, deleting, creating boxes) the linking structure, limits, and Y-scale values. Use the icons and menus to load and process data, and to tailor and print the presentation. Save the redened template in order to reuse it.
Once you have mastered the art of redening templates, it is one simple step further to create your own templates from scratch (templates you can save to reuse as predened templates). To create a template: 1. Create the presentation structure using boxes, links and limits as described below. 2. Load data into this structure. Note: In the Geometry menu, under Features, there are toggle buttons for assigning various features to selected data. Each one has a default (for instance, peak picking is on by default, though it is not always desirable.) 3. Preview the Presentation. Edit it if necessary. Save the new template to reuse it later. 4. Print the Presentation.
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Presentation Manager Boxes

Boxes in Presentation Manager represent data processes (i.e., they are more than a nice way of organizing already processed data.) To work with data or parameter boxes: Use the middle mouse button to draw a box. This box becomes the active box, until you click on another box, which in turn makes the second box active. Use the mouse button to select a box. Use the shift key plus the mouse button to resize a box, dragging the desired edge from within the box. Use the mouse button and drag the box to move it. Use the shift key plus the middle mouse button to delete the box. Once you have created boxes and placed data in them, you may organize how you want this data to appear, setting specic rulers for each box. To set rulers: First, move the boxes until you have the composition you want, positioning them precisely using the four frames at the bottom of the Presentation Manager. The numbers in the four frames indicate the distance of a selected box's four edges from the left, bottom, right, top boundaries of the frame. The numbers can be changed by either typing them directly into the corresponding box or by using the arrows next to that box.
Ruler Links Tool

You may also create links and post limits on different dimensions of the les by using the Ruler Links tool. Links The Links tool lets you create links on different dimensions of the les. Here, Presentation Managers features are dened by the standard that x is horizontal and y is vertical. To create a projection: Rotate the data and link the x axis of one box to the y axis of another box. To invoke the Links tool:
Select
from the Presentation Manager.
To create links between different dimensions from different boxes: 1. Select the target box in the Presentation Manager with the middle mouse button. 2. Select the target ruler from the ruler/link tool. 3. Then, select the source box and source ruler from which you want to link.
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4. Then, click on the Add button to create the link.
Figure 5-53. Ruler Links (Links) Note: Linking only takes place when you preview or plot the data (never before). Limits This button lets you set specic rulers for any box in the Presentation Manager. Using the Limits tool, you can select specic limits on your data geometry. 1. 2. 3. 4. To set a display limit on a ruler: Select the target box in the presentation manager with the middle mouse button. Select the target ruler (X or Y) using the up and down arrows. Then either type the lower and upper X axis limits into the limit input boxes, or use the arrows to adjust the limits. After that, select Add to set the limit.
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To remove a link or a limit: Select the target box and target ruler as described above.
Highlight the item you want to remove in the display box, then select Note: You cannot apply a limit or create a link to the same ruler.
Figure 5-54. Ruler Limits Y-Scale values To set Y scale values: 1. Enter the number of the target box. 2. Enter the number of the source box. 3. Enter the Source Box X Range, either typing in the values or selecting them using the arrows.
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4. Enter the Y scale factor. 5. To set the Y scale values, select Add.
Figure 5-55. Ruler Links (Y Scale) A box may be Y-scale linked to another box. If both are geometries, the rulers in the target box will: Have an X-range as specied by the Source Box X Range. Be centered around the y-position of the baseline from the Source Box. Be scaled (regardless of box sizes) according to the Y Scale factor.
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Previewing the Presentation Once you have composed your data design you may preview how the data will look before sending it to the printer.
To preview a presentation, select A sample preview follows:
Figure 5-56. Presentation Manager (Preview) Printing the Presentation Then you are ready to print the data.
To print a presentation, select
Note: When a box is set as a box link, and IMPORT/TEXT is selected from the menu, the box's type is changed to TEXT_LINK. At the time of plot or display, it finds a file which begins with the filename from the source box, and ends in .txt. For example, if box2 is linked to box1, and box1 has the value: File: EX.2.
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Presentation Manager Menus
box2 will attempt to open and plot the text file EX.2.txt from the user's configured REPORT_OUTPUT subdirectory. This is useful for plotting automatically generated statistical information for geometries.
PRESENTATION MANAGER MENUS

(Study these menus in the help on this tool, page 46-11).
PRESENTATION MANAGER TOOL BAR

The Tool Bar offers quick access to some commonly used functions in Presentation Manager. (For a description of its icons, see help on this tool (page 46-16).
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SIMPLE MODE 1D PROCESSING

If you prefer to use the Simple Mode, toggle off the extended switch in the 1D processor Preferences menu. Once your data is loaded, a 1D Processor window is displayed as shown in Figure 5-57.
Data Source Radio Toggle Buttons Apodization Function Commands
FID display area
Processing Commands
Data processing area
Figure 5-57. Simple Mode 1D Processor
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Simple Mode 1D Processing
Simple Mode Processor Buttons The commands (buttons) for the Simple Mode 1D Processor are described in Table 5-6.
Select: One of these four apodization functions. If no apodization is desired, use Exponential with 0 Hz.
To execute fast Fourier transform (FFT) to convert the data from a time to a frequency domain, transforming it to produce an NMR spectrum. The FFT must be executed before any of the lower buttons will operate. To execute an autophase calculation and display the result in the Phase control panel in the lower right hand corner. You may then ne-tune the phase control if desired. To apply an automatic polynomial baseline correction.
To perform an automatic reference on the data set.
To calculate and display the peaks. The display above or below the peaks may be controlled by turning on or off the Peaks Above in the submenu of the popup menu displayed when the right mouse is pressed on a geometry. To calculate and display the integration.
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Select: To send a plot in the default format to the default printer. The default values are set in the .delta_configure le or by using the Preference Tool. To add parameters to the default plot: select Plot Params in the Mode menu on the Menu bar.
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CHAPTER 6: USING DATA SLATE
Figure 6-1. Data Slate Data Slate (Figure 6-1) is an all-purpose data display and analysis tool that can accept 1, 2, 3 or 4 dimensional data. Data Slate lets you easily overlap and connect data for comparison, analysis, and plotting. For most routine NMR work, 1D and nD processors may sufce. But as you get to know DELTA, you will nd the Data Slate Tool adds dimension, depth and ease to your analyses. This chapter will cover only the basic features of Data Slate: opening a data slate: (page 6-2) loading data (page 6-2) loading multiple data les (page 6-3) overlaying multiple data views (page 6-5) peak picking, data reduction and integration (page 6-14) peak deconvolution (page 6-14) annotation (page 6-14) advanced data slate operations (page 6-15) More information is provided in on line help for this tool (or see page 22-1). Note: Data Slate also forms the basis of the 2D, 3D, and 4D viewer tools, and the 3D-Slicer. Those tools, and the TSC (tubeless sample changer viewer) Tool
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Chapter 6: Using Data Slate
procedures are all discussed in the online help (Delta Users Reference Guide). To open a Data Slate: 1. First select the Data Slate icon from the Delta Console menu. The Open Data for Data Slate window will appear. 2. From the list of les in this window, make a selection and select OK. The Data Slate will appear, with its menu bar and icon buttons.
LOADING DATA INTO THE DATA SLATE

Data Source Toggle Buttons
To the far left of the Data Slate menu bar (see Figure 6-1) there are two icon buttons, one with a disk and one with a nger. Since one of these two buttons is always selected, they act as a toggle to determine the source for additional data. When the disk icon is selected, data will be retrieved from a disk le. When the nger icon is selected, the data will be retrieved from another screen window. To load a Data Slate from disk: Click on the Open File folder icon . Or select Open File (Ô) from the File menu in the Menu bar.
To load a Data Slate from an open window: If the nger icon is depressed, data can be loaded directly from another window. Click on . Click the mouse button on any data displayed on the screen. The data will be loaded into Data Slate.
To Load Data Files using Drag and Drop Click on a le with the right mouse button. Then before the dragon disappears, click on the desktop. This will open a Data Slate with a Data Geometry in it (page 22-1). To load a second le into the Data Slate, click on a Data Geometry with the right mouse cursor button, then click on the open Data Slate.
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Loading Multiple Data Files
LOADING MULTIPLE DATA FILES

One of the powerful features of Data Slate is its ability to display multiple data les simultaneously. Currently, up to 16 separate data sets can be displayed. The data les can have any dimension, frequency and data density. As new les are loaded, the Data Slate will automatically tile the data to ll the space in the display area. The data source can be changed at any time to load data into the same Data Slate window from either a disk le or a display area. Horizontal and Vertical Views When multiple data sets are loaded, Data Slate will automatically tile the window to accommodate them. Set the tile format either to vertical or horizontal mode under the View menu (Figures 6-2 and 6-3).
Figure 6-2. Vertical Data Slate Views
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Figure 6-3. Horizontal Data Slate Views Box Data View Select the Box option under the View menu to tile all the data windows to an equal size (Figure 6-4). This option is meaningful only if there are more than two data sets loaded.
Figure 6-4. Box Data Slate View
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Selecting Active Data Sets
In the Preferences Tools Page you can set the preference Data Slate: View Orientation to orient geometries in the Data Slate horizontal, vertical, or box. Defaults to horizontal.
SELECTING ACTIVE DATA SETS

A Data Slate can have multiple data sets inside a single window, but the Cursor and Level Tools can adjust only one data window at a time. The active data geometry window is called the active or selected data. To select the active data set: Put the cursor in a window and click the mouse button. The mouse pointer will turn yellow. When working with multiple data sets inside Data Slate, always check to see that you have the correct data set selected with the mouse and that the mouse pointer has turned yellow. To remove a data set: First select the data, then click on will be resized to ll the entire window. . The data will disappear and the other data sets
The trash can icon will not delete the data from the disk, but any changes made to the data will not be saved. To save changes to the data set you are removing:
Select
before selecting
To overlay multiple data sets: Select . Either the Open File window or the Finger will appear, depending on
the data source selected (disk or nger). After the le is selected, it will appear in a color which contrasts with the existing data (see Figure 6-5). Each data window in Data Slate can have up to 32 overlay data sets. The colors can be changed by using the Level Tool. Consult the Users Reference Guide (page 22-6) for more information. Overlaid data sets do not need to have the same number of data points or spectral width, or be collected at the same magnetic eld strength. The only requirement to overlay data is that the data sets be correctly referenced.
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Overlaid data is aligned using the axial unit reference values. If a data set is not referenced properly, use the reference features in 1D Processor or the Reference Tool to correct the problem.
Figure 6-5. Data Overlay To select a data set from among the overlaid data: Use the Select cursor mode. Then select a data set with the mouse in the overlaid data window, and select this mode:
The colored triangles in the lower left corner will change to reect the active data set, and the lename with all overlaps checked will show at the top of the lename list. Note: This selection method will just step through the overlays, so use caution if you have more than two data sets in the window. To remove a single overlaid data set: Use the Select cursor mode to make the desired data set active; then select remove the data. to
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Data Slate Icons
To remove an entire data window: Select .
DATA SLATE ICONS

A summary of the Data Slate icons follows: Table 6-1: Data Slate Icons Select: Use these three icons in determining data destination: To load new data into the current Data Slate and re-tile the data windows (default). To replace with new data the currently selected data displayed in the current Data Slate. If multiple data files are displayed, the data in the selected data window will be replaced. To create a new data slate by loading new data into a new Data Slate window that is spawned as a separate process. For other operations on data (make sure the cursor is yellow): To disallow loading of high resolution data into the slice or projection geometries. This only shows up when the Data Slate is in Template mode. To load data into Data Slate from disk.
To overlay multiple data sets.
To remove a data set, rst select the data, then click the Trash can icon on the Menu bar. The data will disappear and the other data sets will be resized to ll the entire window. Also use this icon to remove an entire data window.
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Table 6-1: Data Slate Icons Select: To remove a single overlaid data set: Use the Select cursor mode to make the desired data set active. Then click the Erase Overlay icon to remove the data. To save the processed version of the le to disk.
To plot the geometries that are displayed in Data Slate (or send its plot to a le.) This window gives you 20 seconds to change print options, e.g. to redirect a plot to a network printer. It automatically prints the geometry if you dont click OK or Cancel.
Figure 6-6. Print Options To automatically peak pick and integrate the spectrum. Searches for all peaks in the le. This operation is the equivalent of auto analyzing the le using 0 hertz as the cosy parameter and whatever is set for the integral width. Note: you cannot see these peaks until you turn on the peak pick information in the Options Menu. To search for all peaks in the le and performs integration.
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Data Slate Icons
Table 6-1: Data Slate Icons Select: To step one slice backwards.
To step one slice forwards.
Note: For the arrow buttons to work:
After slicing, the specic Slice display area must be active. After expansion, the 2D contour display area must be active. The locations of the expansion slices are marked on the axis of the 2D data.
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The File Math Tool The File Math tool may also be used to perform math operations on one or two les, and then place the result into a new, or existing, Data Slate.
Format label Equation label Operator enumeration
Unary enumerations
Constant Input Boxes
To invoke this tool: Select the File Math command found in the Tools menu of Delta Console, under Math. The Format Label shows the format of the le math equation. The Equation Label will remain empty until the le buttons have selected the les on which File Math will operate. # of Files allows you to perform math operations on either one or two les. When math operations are done on two les, the two les are combined using a simple mathematical operator. Operator Enumeration (+, or - or * or /) lets you choose how you want to combine operations on two les. Destination Button toggles between placing the resultant le into a new Data Slate or into an existing Data Slate. To place the resultant le into an existing Data Slate: you must choose the Data Slate to which you want to add the le. To do this, click on the menu bar of Data Slate with the selection nger cursor (which appears when you click on the destination button).
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Connected Objects
Use File Buttons to select the les on which you want to perform math operations. When you click on a le button, the le button will turn red and the cursor mode will change to the selection nger. Select a le by clicking on its geometry with the selection nger. This places the name of the le selected in the geometry inside the button and turns the button green. If the selection fails, the button turns blue again. The le button that selects le B is disabled when the number of les is set to one. Likewise, if the number of les is set to two, then the le B button is enabled. Use Unary Enumerations to select a unary operator that will act on the le. There is a long list of unary operations that can be performed. If you select NONE as the unary, then no unary operation will take place. Constant Input Boxes are used to enter constants displayed in the format label. Select to see the transformed data in the Resulting File window:
Figure 6-7. Resulting File Window
CONNECTED OBJECTS
The Connected Objects feature allows multiple data sets to be expanded and analyzed. The data may be in the same or different windows. The data sets do not need to have the same number of data points, spectral width, magnetic eld, or be in the same window. The connection is done on the axial unit reference value. Because some connections are done on the axial units, the data must be properly referenced. Use the reference features in 1D Processor or the Reference Tool to correct alignment problems. To connect Multiple Data Sets 1. Invoke the Connection Tool by clicking on . 2. Click the Select 1 button (see Figure 6-8). The cursor will change to the nger mode, .
DELTA Users Guide, v 3.2 6-11
3. Move the cursor and click on one of the data sets. The nger mode cursor will change and the lename on the selected data set will be displayed in place of Select 1" on the button. 4. Click the Select 2 button. The cursor will change to the nger mode .
5. Move the cursor and click on a second data set. The lename of the second data set will be displayed in place of Select 2" on the button (see Figure 6-8.) 6. On the Connection Tool, the axes of the rst data set are listed at the top of the columns; the axes of the second data set are listed below. Select the axes to be connected. Other combinations of axes may be selected depending on the data types or connection desired. 7. Click the Connect button to complete the connection. 8. Repeat steps 1-7 to connect additional data sets. After data sets are connected, any function applied to one of the windows should appear in the other window(s) simultaneously. Features that can be toggled off, such as cursors, must be turned on under the Data Slate Options window to be seen. Several other features can be connected. See Features on the Menu Bar of the Connection Tool. For more information, consult online help on this tool (page 19-1).
after before
spec_1 X connected to spec_2 X 1st Data Set Axes 2nd Data Set Axes
Figure 6-8. Connection Tool after and before a Connection is Made Individual Data Presentation Control All of the data sets inside a single Data Slate window share the same display options. This means that if one of the spectra has the peak picks or integration option active, then all the spectra in the same Data Slate will also have those options active. To turn display options in different data sets on or off: Use the popup menu on the Data Geometry. Move the cursor to that data geometry, then select the right mouse button to bring up the data geometry options window.
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Connected Objects
TO PERFORM OPERATIONS ON THE DATA GEOMETRY USING OPTIONS: Note: Data geometry Options are quite often used in conjunction with the Mouse Cursor Tool. Use the Options menu to perform all operations on data geometries that you can perform in Delta processors (see page 5-60): Panning, Rotating and Expanding Data The Geometry Tool can also be used to pan, rotate, and expand the data in a geometry.
Figure 6-9. Geometry Tool To invoke the Geom tool: Select the Geom Tool command found in the Tools - Geometry Tool menu of the Delta Console. Select: Select Geometry to work on a geometry with the tool. When you click on this button, the cursor mode changes to the selection finger. Clicking on the geometry with the selection finger will connect the geometry to the tool.
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Speed Enumeration is used to control the precision and speed of the Geometry Tool. The higher the number, the faster the tool will work. However, the higher the speed, the larger the jump for panning, rotating, and expanding.
PEAK PICKING, DATA REDUCTION AND INTEGRATION

When data is loaded into the Data Slate, all the information is loaded with it. If a data set has been previously peak picked or integrated in a 1D Processor, for example, and the data is loaded into the Data Slate, the peaks and integrals can be displayed simply by turning on the corresponding option. In the Data Slate, peak picking and integration (either automatic or manual) are done identically to the methods used in the 1D Processor. Please refer to Chapter 5. Peak Deconvolution When data is loaded into the Data Slate, all the peak deconvolution information is loaded with it. If a data set has been previously deconvolved in a 1D Processor, for example, and the data loaded into the Data Slate, the deconvolution can be displayed simply by turning on the corresponding option. In the Data Slate, peak deconvolution is done using methods identical to those used in the 1D Processor. Please refer to Chapter 5, page 5-51.
ANNOTATION
Annotations are also kept with stored data. Annotations in the data set can be displayed simply by turning on the corresponding option. In the Data Slate, Annotation is done using methods identical to those in the 1D Processor. Please refer to Chapter 5, page 5-55.
SPREADSHEET TOOL
The Spreadsheet Tool is used to display and print peak, integral and assignment information. In the Data Slate, the Spreadsheet Tool functions the same as in the 1D Processor. Please refer to Chapter 5, page 5-64.
PLOTTING DATA
Please refer to Chapter 5, page 5-67.
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Connect Options on the View Menu
CONNECT OPTIONS ON THE VIEW MENU

These connect options simplify data analysis by applying the same functions to all open geometries. They are all options you select under the View menu on the Data Slate. Note: Connect X and Connect All can either be toggled, or both turned off.
Table 6-2: Connect Functions Select View To connect all currently open geometries in the X dimension. With this feature active, you can zoom in on all geometries in the X dimension only, or apply functions like cursor and region in the X dimension only. To connect all currently open geometries in all dimensions; for example, X and Y dimensions will be zoomed for all currently open geometries. To apply any function selected from Options menu across the board. See page 6-13. To save whatever connect options you check during a session.
Connect X
Connect All
Connect Features Connect Saved
ADVANCED DATA SLATE OPERATIONS

The Data Slate has two advanced presentation features: the Slicing and Expand options. These options are used with multi-dimensional data sets, either 2D, 3D, or arrayed parameters. The Project option is not active in Data Slate. It is used only in the 2D viewer tool. Slicing The Slicing option (also available in 2D data viewer) works with the Pick cursor mode.
For example, in Pick mode when the pick cursor is positioned on a 2D data set, both an X and Y slice, if selected that way, would be loaded into the Data Slate window (Figure 6-11 shows an example where the Y slices are selected). Move the slice select positioning guides in the 2D contour map by holding the mouse button down. When you release the mouse button, the X and Y slices will be updated. Select the dimensions from which the slices are picked under the Slicing menu Set Dimensions option (Figure 6-10). For example, to generate a set of specic X domain slices, select only Slice by Y.
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After picking the slices, use the left/right arrow buttons on the Data Slate tool bar to step back/forth by one slice increments through the 2D data. This helps you examine neighboring slices of data. The arrow buttons will work only when the specic slice display area is active. You can tell if the slice is selected by the color of the cursor when it is positioned over the map. In the default color scheme, the cursor will turn to yellow over a selected area and turn to red over areas not selected. Use the right mouse button to select an area when the Pick cursor mode is enabled.
Figure 6-10. Data Slate Slicing Menu
Figure 6-11. Data Slate Slicing
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Advanced Data Slate Operations
Expansion The Expand option in the Expansion menu takes a 2D data set and performs a multiple slicing operation, pulling out the specied number of contiguous slices (Figure 6-11). Specify the number of expansion slices by using the Expand... option (Figure 6-12). The Expansion menu is shown in Figure 6-12. The initial starting position for the Expansion is set at the edge slice of the 2D object that you are expanding. After the initial expansion, select these buttons on the Data Slate tool bar to step through the expansions through the 2D data. The locations of the expansion slices are marked on the axis of the 2D data. The 2D contour map area must be the active area for the arrow buttons to work. You can tell if the 2D contour map is selected by the color of the cursor when it is positioned over the map. In the default color scheme, the cursor will turn to yellow over a selected area, and turn to red over areas not selected. Use the right mouse button to select an area when the Pick cursor mode is enabled. The linearize function lets you take the current view of a multidimensional le (Figure 614) -- from the X dimension -- and place them end to end. It operates on an nD data set to compute (in the simple case of X and Y data) Y abundance for a given X. Do not disturb a Data Slate while it is trying to create, refresh, or delete an Expansion display! All other DELTA windows will not be refreshed until the Data Slate is allowed to nish.
Figure 6-12. Expand Options Menu
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Figure 6-13. Data Slate Expand Display
Figure 6-14. Expand Size Selection Use the Connection Tool to connect slices or group expansion display areas (page 6-11).
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INTRODUCTION
Two dimensional NMR data is processed with a specialized tool called the nD Processor. As the name nD Processor implies, the tool is designed to process and display data sets from 1 to 8 dimensions. This chapter will cover only basic 2D processing: Loading data (page 7-1) Preparing processing lists (page 7-6) Loading and processing 1D slices (page 7-9) Phasing data (page 7-10) Viewing data (page 7-13) Contouring data (page 7-17) Plotting data (page 7-30.)
The nD Processor displays one processing list column for each dimension. Each dimension is treated as a separate processing list. From any dimension, the user may examine a 1D spectrum along that dimension with the 1D Processor. Before using the nD Processor, the user should be familiar with the 1D Processor and Data Slate tools. For a more detailed discussion of nD processing, refer to chapter 9 of the Delta Users Reference Guide.
LOADING 2D DATA INTO THE ND PROCESSOR

To invoke the nD Processor, select: in the Delta Console Tool Bar, A new window to Open Data for Processing will appear (see Figure 7-1). Browse the directories and select the two-dimensional le to be processed.
7-1
Current Directory Name List of Subdirectories List of Files
File Info Name of Selected File
Figure 7-1. Open File If the nD processor is already running, or if you call nD processor from the Processors menu on the Delta console:
To load new data, select . Or, select Open (Ô) under the File menu in the Menu bar.
To open a new nD le and remove the current processing list, select Processing a 2D data set begins with an empty 2D Processor.
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Elements of 2D Processing
Figure 7-2. Empty nD Processor
ELEMENTS OF 2D PROCESSING
DELTA software treats each axis of an NMR data set as a domain. A domain has a nucleus type, spectral width, and processing parameters. An NMR data set may have only one major domain at a time. All other domains are called minor domains. In order to eliminate confusion about the order of t1, t2, and t3 evolution times in NMR data, DELTA uses the nomenclature x, y, z, , , , , to specify the domain. The x domain is always the dimension collected by the spectrometer receiver. The y dimension is always the next slower incrementing domain, z the next slower, and so forth. Processing can occur only on the major domain of a data set. The Transpose command interchanges the major and minor domains through a cyclical rotation. For n dimensional data, after n applications of Transpose, the major domain will be back to the starting location.
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The active domain is selected by the button at the top of each column. Click the button (X or Y in Figure 7-3) to change the active domain. Only the processing list of the active domain may be edited. If you want to partially process a data set, leave the processing lists empty (except for Transpose) for those domains you do not want to process. The higher domains are controlled by the buttons at the bottom of the nD Processor window. Up to 4 domain lists can be viewed at once.
Slice Constrained Input Boxes
Processing Lists
Parameter Domain Control Button
Domain Buttons
Figure 7-3. nD Processor Window
7-4
Preparing 2D Processing Lists
PREPARING 2D PROCESSING LISTS

Processing a 2D data set begins with an empty 2D Processor. 1. Each domain of a 2D data set has a separate processing list. Normally, the domains are processed from left to right; i.e., X then Y for a 2D data set. 2. Each processing list column must end with the [transpose] command that changes the major domain prior to going to the next domain. 3. The [transpose] command, like the Display/Phase command in the 1D processor, cannot be removed from the list. 2D processing lists resemble 1D processing lists (see Chapter 5). Like 1D processing lists, they may be constructed by selecting items from the Menu bar. Use the icons and command buttons on the nD processor for copying, composing and editing your processing lists. See the discussion on the nD Processor in The Delta Users Reference Guide for a detailed listing of these icons and menus.
X domain list selected
Figure 7-4. X-Domain processing list
To read a 2D processing list from disk, select Processing lists may be stored and recalled from disk, just as in 1D processing, using this icon, or the Open List option under the File menu.
To save a new list, or modify an existing list, select or the Save List option under the File menu.
You can create a new 2D processing list analogous to the way 1D processing lists are created, by selecting operators listed under the pull-down menus. To create a 2D processing list using the menus: 1. Select a topic on the Menu Bar. 2. Hold and drag the mouse to highlight the desired option or command. 3. Release the mouse button and the option will appear in the processing list. You can use your rst processing list as the basis for the second Select: To designate a disk le as source.
To designate another Processing window as source. Both this icon and the Open File work with the Open List icon to load the Processing list. If the processor is already running, load new data by selecting either this Open File folder icon or Open File (Ô) from the File menu. Select this Open File Clear icon or Open Clear from the File menu to load a new le and remove the current processing list. To open a processing list from the source. If the source is set to from disk, the Open File Tool will appear. If the source is set to from another window, the mouse pointer will change to and the user must click on the window containing the desired processing list. To save the current processing list to disk. The Save File Tool will appear, and the user will be prompted for a file name. To print the processing list.
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Preparing 2D Processing Lists
To edit a Processing List
Select: To place the next processing item at the end of the current list. Even if a processing step is highlighted, the next selected item will be placed at the end of the list. To place the next selected processing item before the selected item in the list.
To change the selected item to the next item selected from the pull-down menu.
To cut the selected line from the processing list.
To paste a cut item at the selected location in the processing list. Note: Cut and Paste are local to the processing window. You can not cut and paste items between different processing windows. And you can also use the drag and drop dragon to create a processing list: Select the widget from which you want to copy data. Then, hold down the right mouse button (or select Ctrl left mouse button). Before the dragon symbol disappears, move the cursor from the selected widget to the widget into which you want to copy the data, and let go of the button. To erase the contents of the selected processing list.
7-7
Select: To delete the currently selected (highlighted) item in the processing list. All subsequent items will be renumbered.
To copy an entire processing list from a different dimension of the nD Processor. Select rst the source domain button (e.g. X), then the Copy button, then the destination domain (e.g. Y). Note: Each domain of a 2D processing list must end with the transpose statement, which causes the data to be phased and displayed in the window. To start up a 1D Processor and load a 1D slice of data.
To process data and put up to 16 slices in Data Slate.
Selecting a Data Output destination After the processing list is set, select the output destination for the data using the icon buttons to the right in the row of icon buttons (Figure 7-5). The destination may be a Disk File, 2D Phasing Tool, Data Slate, or 2D Viewer. Clicking on the destination button initiates the processing. During processing, the status is displayed in the Delta Console.
2D Phasing Tool Disk File Data Slate 2D Viewer
Figure 7-5. nD Process Data Destination Buttons Delta never processes or modies the original data. It always makes a copy rst, then processes the copy. Therefore when large multi-dimensional data sets are processed, there may be a delay while the copy occurs. During the copy, a message is displayed in the Delta Console.
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Loading and Processing 1D Slices
Toggling between processing list view and geometry view:
Select: If processing needs to be done, then the data will be processed when switching to the geometry view. Selecting Preferences TO SELECT PREFERENCES: Selecting PreferencesPlot Params Plots parameters with the le. Plot Process List Plots a processing list with a le. Plot Pop-Up When On, a printer dialog pops up when a request is sent to plot data.
LOADING AND PROCESSING 1D SLICES

Often it is desirable to look at a particular vector or 1D slice from a multi-dimensional data set during processing. Delta allows the user to extract any slice from the data set, process the slice as a 1D spectrum and use the 1D processing list in multi-dimensional processing.
To load a 1D slice of data parallel to any dimension: 1. Select the column for that domain by clicking on the domain button at the top of the processing list. The indexing value for the other domain(s) will determine which slice is displayed. 2. Click on the 1D Slice button. 3. A 1D Processor will start up and the slice will be loaded. If a processing list for that domain already exists, it will be copied to the 1D Processor and executed. 4. After the 1D Processor opens, create a processing list or make changes in an existing list in the 1D processor as you would for 1D data. 5. When the processing list is correct, select Quit under the File menu to close the 1D Processor. The 1D Processor will close and the processing list will be transferred automatically to the nD processing list. 6. Use the Y slice button to process data and put up to 16 slices in Data Slate.
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PHASING 2D DATA
If 2D data is collected in phase-sensitive mode, it may be phased in both dimensions to give in-phase absorption mode display. Phasing is not necessary (or possible for that matter) in the case of absolute value or magnitude 2D data. Phasing can be done in several ways: in the processing lists by phasing the 1D slices, on the 2D spectrum by picking slices and processing them with the 1D Processor, or on the 2D spectrum using the 2D Phasing Tool. The choice of the phasing method depends on the experiment and sample. If the data has been baseline corrected or compressed by the Real command, the imaginary data has been deleted and the phase cannot be adjusted. Reprocess the raw data and make the phase corrections before the baseline corrections or before using the Real command. 2D Phasing Tool The 2D Phasing Tool is shown in Figure 7-6. The 2D Phasing Tool allows the user to interactively phase 2D data while observing the contours. Data may be loaded into the 2D Phasing Tool by using either the nD Processor destination buttons (see page 7-8) or
on the menu tool bar. The rst (target) le view displays the entire le. The second (regions) view displays the phasing for characteristic portions of the le. Note: Phase 2D will not save the phase corrections until you choose Save from the File menu.
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Phasing 2D Data
Figure 7-6. 2D Phasing Tool To invoke the 2D phasing tool: Select the Phase 2D command found in the Processors menu of Delta Console.
Or select found in the nD Processor or the Process Tool. However, in these cases, the data le is rst processed by the tool it is in, and the result is placed in 2D Phaser. To use the 2D Phasing Tool: 1. Select regions with the middle mouse button and the Region cursor tool (F3). You may also select Region in the scroll down list for this tool. If you do so, a box will appear around each region selected. 2. Or, select and draw the region. White index marks showing the boundary of the region will be displayed on the axes. The region can be moved freely in the display area. Up to 4 regions can exist at any moment.
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3. Press and the display will change to Figure 7-7. 4. Use the X and Y/ P0 and P1 input boxes to adjust the contours so they are in-phase. 5. Press to apply the current phase corrections to the data. The P0 and P1 values displayed in the input boxes will be reset to zero. 6. Use Transfer on the Menu bar to transfer the data to either a 2D Viewer or a Data Slate after phasing is completed. For a full discussion, consult help on the 2D Phaser (page 43-1).
Figure 7-7. 2D Phasing Tool Region Display
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2D Viewer Tool
2D VIEWER TOOL
Figure 7-8. 2D Viewer - Contour Mode The 2D Viewer is a version of Data Slate specially designed for optimal display and analysis of 2D data. 2D data is displayed as a contour map in the middle of the window. Space is reserved for projections and slices along the top and side. You can select a 1D data display area of the window and load a 1D le into any of the projection or slice areas (see page 7-18). The cursor turns yellow to mark an area into which data may be loaded. For more information than what is provided here, consult online help on this tool (page 81). When the 2D Viewer is rst started, the areas reserved for slices are displayed as the projection data until you select the Pick Cursor and choose data slices. The 1D data labels are always in the base units of the 2D data le. If you change the display labels with the Rulers menu, the le units displayed with the slices are not affected. There are three ways to start the 2D Viewer Tool: 1. Start it directly from an nD Processor by selecting loaded after processing is completed. . Data is automatically
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2. Start it by selecting
on the Delta Console. A new window called Open File
will appear (Figure 7-1 on page 7-2). From the Open File Tool, select the le to be viewed. 3. Start it from the Viewers menu in the Delta Console. When the 2D Viewer is started from the Viewers menu, it will appear empty until data is loaded. To load new data with the Viewer already running:
Use the Open Folder icon
or select File, then Open File (Ô) in the menu bar.
To load data in from another window to the 2D Viewer: Use the Finger icon and select the data geometry you want to load.
Once data is loaded, you can set the level of the contour lines in the 2D Viewer window, if necessary (see page 7-17). Two Dimensional Display Modes To view two dimensional data in different display modes: 1. Press the right mouse button on the data window. 2. From this Main Display Area menu, select the desired view. Select: Contour (default) Mesh Surface Stack To map the 2D data as Contour lines controlled by the Level Tool (a maximum of 24 negative and 24 positive levels). To map the 2D data to a wire frame surface to create a 3D object. The 3D object may be rotated and zoomed. To map the 2D data to a 3D surface. The object may be rotated and zoomed. To draw the 2D object as a set of 1D spectra. The stacked object may be zoomed and panned, but not rotated or viewed from different angles. Stack mode does allow the user to change the x and y offset between slices to better see relationships between slices. Displays the 2D data set as an intensity/brightness map.
Image
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2D Viewer Tool
Select: Datadex nD To display an nD object as a series from n=1 to (n-1)D spectra with the ability to rapidly step along the axes and move between different dimensional levels.
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(a)
(b)
(c)
(d)
Figure 7-9. Mesh(a), Surface(b), Stack(c), and Image(d) Modes
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2D Viewer Tool
2D Cursor Tool functions The Cursor Tool functions in 2D are identical to those used in the 1D display mode. Refer to the Delta Users Reference Guide for a fuller treatment of the Mouse Cursor Tool on page 4-1. Contouring 2D Data Because the contours are calculated in advance, you can zoom and pan the data in realtime. Data will be automatically contoured when it is loaded into 2D Viewer, since the default viewing mode of 2D data is contour. If the contour levels are not satisfactory, use the Level Tool to adjust the position and number of contours. The Level Tool allows up to 24 positive and 24 negative contour levels. Individual contour levels may be turned on or off by clicking the level buttons with the mouse. The position of the contours is controlled by the contouring function. The contouring function is controlled by the Start and Bias controls. Use the mouse to drag the Start and Bias control sliders. When the Start and Bias are altered, the current contour buttons will be grayed-out, and the Apply button must be clicked to recalculate the display. To improve the interactive performance, all of the selected contours are calculated at one time. If the Level Tool is not already open: Move the mouse pointer into the 2D data display area in the 2D Viewer window. Then press the right mouse button to display the pop-up menu, and select Level Tool. The Level Tool window opens.
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Contour-line Buttons s Bias Box Preset buttons
Bias Slider
Start Slider Plus and Minus buttons Apply Button Peak threshold Noise threshold Baseline
Negative contours Positive contours
Start sliders
Figure 7-10. Level Tool Determines the minimum intensity of the bias. Set these so that the base level is positioned at the bottom of the Level Tool window.
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2D Viewer Tool
Adjust the number of contour levels drawn by clicking on the contour-line buttons in the Level Tool window. Sets the number of contour lines. 2,4,6,8,12, 16 and 24 may be preset.
Preset buttons
Contour-line level buttons Bias slider
The level can be set manually by clicking on each button to highlight it. Determines the slope of intensity. If the slider is located near the top of its range, a lot of contour lines are drawn at the low end of the spectrum. See below. Adjust the number of contour levels drawn by clicking on the contour-line buttons in the Level Tool window. The levels of the contour lines are set based on the noise level, automatically obtained after data processing is completed. Only the colored buttons have been computed. Changing Contour Levels The levels of the contour lines are set based on the noise level, automatically obtained after data processing is completed. Only the colored buttons have been computed.
Often the threshold for the 2D display must be adjusted for optimum presentation or to observe crosspeaks of lower intensity. The contour algorithm is an exponential function and has two adjustable parameters: Start and Bias. These are displayed as sliders on the right side of the Level tool. Bias adjusts the spacing between adjacent levels. Start adjusts the starting position. Use the mouse to drag the Start and Bias controls. When Start and Bias are altered in any way, the current contour levels are grayed-out and the Apply button must be clicked to recalculate the display. If you accidentally move the Start or Bias control, click on the 2D spectrum with the Select mode cursor and the Level tool will return to the current view Start and Bias values. The Delta Users Reference Guide (online help) describes the Level Tool in greater detail (see Level Tool on page 5-1). To change or compute new contours: Click on a grey contour-line button. Click on the Apply button in the Level Tool window. The contour lines are redrawn. Note: If you try to draw contours too far down into the noise, a dialogue box will pop up informing you that it will not draw all the points asked for. This is to guard against bogging down the computer. Selecting the appropriate settings for the Level Tool is important, as seen in the following demonstrative examples.
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Figure 7-11. Data with too few (only topmost) contours selected
Figure 7-12. Data with too many contours selected (well into the noise oor)
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2D Viewer Tool
Figure 7-13. Data with a sensible distribution of contours selected If you have calculated a contour that is too low into the noise, you can simply turn off that level display by clicking on the appropriate Contour Level button on the Level Tool. The Contour Level button will appear to pop up and that selected contour level will immediately turn off in the display. The Contour Level button will remain colored, indicating that level has been calculated. To view it again, simply click the same colored button. Display positive and negative contour levels independently using the (+) and (-) buttons at the bottom of the Level Tool. These buttons will turn on or off all of the Contour Level buttons in the associated column.
Overview Area In the upper right hand corner of the 2D Viewer is the Overview. This is a small window that always shows the entire data set. If the display has been zoomed, the zoom area is indicated by a rectangle in the Overview display. The Overview is an active data area; zooming and panning can be done from this area. Zooming and Panning 2D Data The mouse is used for zoom and pan control with 2D data as well as with 1D data. To use the zoom: 1. Select Zoom mode (F1) on the Cursor Tool.
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2. Then select to select a rectangular area from the 2D data. 3. You may also use Zoom directly on the Overview area to move the box outline, create another zoom area, or reshape the zoom area. 4. To Zoom on only one dimension of the 2D data, click and drag the mouse button in either axial ruler area. The rectangle will be drawn over the entire 2D display between the points on the axis selected by the mouse drag. To pan across the data: 1. Select Zoom cursor mode. 2. Select this operation and drag the mouse in the axial ruler area. A slider control will appear as a reference when you are panning. 3. After you have nished panning, the Overview area in the upper right corner of the window will be updated to show you the current zoom area as a small rectangle overlaid on the entire map. Note: You can pan the rectangle directly in the Overlay area. The Pan function is active in the main display; the horizontal and vertical pan are selected by the mouse position. An imaginary 45 degree diagonal line from the lower left corner separates the Pan horizontal from the Pan vertical area. 4. To return to the previous view: press the Backspace key. The zooms and pans are kept in a history list and the Backspace key moves back one level at a time. 5. To return to the full spectrum: press the Home key. Slice and Projection Areas When the 2D Viewer is initialized, two separate areas are reserved along each axis. Both of these areas are initialized with the data projections. The Display option on the Menu bar allows the user to turn these areas on or off independently. The area closest to the 2D data, called the Slice area, is updated each time a Pick is made by the mouse. The outer area, called the Projection, is updated when a projection is done. To nger high resolution 1D data into either the slice or projection areas: Select the menus under Display - High Res. The high resolution data does not need to match the 2D data in data points or spectral width. Alignment is done by the axial reference point; therefore, the 1D and 2D data must be referenced to the same peak in either Hz or ppm.
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2D Peak Pick and Data Reduction
Note: If the high resolution 1D data does not line up with the 2D data, check the spectrum reference. When the data is newly loaded into the viewer, press the home key once to reset all expansions. If the data reference must be changed, use the normal procedure for either 1D or 2D data.
2D PEAK PICK AND DATA REDUCTION
To peak pick and integrate (in both 2D and 1D processing), select To view the peaks:
1. Select Peak Pick from the popup geometry menu. 2. If no peaks are displayed, it is because the data doesnt contain peak information. Select to recalculate and refresh the display. Peaks will be displayed as octagons with the peak width in each direction represented by a pair of crossed lines (Figure 7-14 and Figure 7-15). 3. Select peaks with in Peak mode, dragging the mouse with the mouse button depressed across the peaks of interest. Selected peaks will be displayed in yellow.
Figure 7-14. Peak Pick Overlay
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Figure 7-15. 2D Peak Pick Display To manually add a peak: 1. In peak mode of the cursor tool, select then select the peak. If the desired
peak does not meet the threshold and noise criteria, a message is displayed. If this happens, select to force a peak to be created.
2. Or, adjust the threshold and noise level using the Level Tool, and select the peak again. 3. Hold down the right mouse button when over the data and select Statistics from the Options menu. To manually delete a peak: 1. In Peak cursor mode, select and click on the peak. in Peak mode, or by
2. Select peaks in addition to a selected peak by selecting
clicking on individual peaks with the mouse button while depressing the SHIFT key. The selected peaks will be colored yellow. To delete this group of peaks: Type d on the keyboard.
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Peak Grouping Very often, in multidimensional data, the cross-peaks exhibit ne structure and the peak pick algorithm may label each peak inside the multiplet as a separate peak (Figure 7-16). However the ne structure is often unnecessary for basic 2D analysis.
Figure 7-16. 2D Peak Multiplet with Fine Structure To simplify data by grouping it: Select individual peaks with the Peak cursor and type the letter g on the keyboard. The selected peaks will be replaced by a single peak (Figure 7-17) centered at the average position of the selected peaks. The resulting diameter of the grouped peak indicator is the centers of the original peak indicators; therefore, the diameter is an indication of the apparent J coupling constant.
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Figure 7-17. Peak Grouping Peak Melding Peak melding is similar to peak grouping, but in this case the width of the new peak lies outside the constituent peaks (Figure 7-18). The resulting diameter of the melded peak indicator is the outside limit of the original peak indicators.
Figure 7-18. Peak Melding
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Integrating 2D Data The integral features of 2D are very similar to 1D data (see Figure 7-19). Although the individual peaks are automatically volume-integrated when a peak pick is done, the user
may create an arbitrary integral using in the Integration mode of the Mouse Cursor Tool. The integral limits are rectangular and the bounds are forced to the nearest data point. Individual integrals can also be deleted by selecting .
When the integral rectangle is selected it will change to yellow. You can also hit the Delete key to remove this integral.
Figure 7-19. 2D Integration. Annotating 2D Spectra Annotation is performed with the cursor Text mode. To display the annotation (Figure 720), the Annotation option (ALT A) must be selected in the popup geometry menu. If the annotations do not remain displayed on the screen, check that the Annotation option in the Options menu on the popup geometry menu is selected.
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Figure 7-20. 2D Annotation To create an annotation: 1. Locate and expand the peak of interest.
2. Place the mouse pointer in the Text mode and select to type text at any location you select. 3. Greek characters can be created using the ALT key with the appropriate English letter. Annotations are limited to a single line of text. 4. Type Enter to stop annotating. To edit an existing annotation:
1. Place the mouse pointer in Text mode. 2. Select the annotation with the mouse button. The annotation will turn yellow.
3. Select to edit the annotation. 4. Select Enter to terminate the editing session.
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Rotating and Shifting Annotations Annotations may be rotated and shifted (anchored) about the insertion point. The rotation and shifts may be done at any time in any order. To rotate an annotation: 1. Place the mouse pointer in Text mode. 2. Select the annotation; it will turn yellow. 3. Press the Page Up keyboard key to rotate 90 right (up) or Page Down keyboard key to rotate 90 left (down). To shift an annotation: 1. Place the mouse pointer in Text mode. 2. Select the annotation; it will turn yellow. 3. Press the Home key to right justify the annotation or the End key to left justify it.
4. Select this operation To change annotation fonts:
to move the text.
Greek characters can be generated by holding the left ALT key and typing in the appropriate key (a= alpha, b = beta, etc.) You can bring up a menu to change the font/attributes/size of annotations by selecting
then selecting the text, then using the mouse cursor to bring up a selection menu. Or use these key combinations: Select: Shift - arrow key to change the font. Ctrl - arrow key to change the font size. Alt - arrow key to change the font attribute.
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Fields
Figure 7-21. 2D Spreadsheet Spreadsheet Tool The Spreadsheet Tool is used with multi-dimensional data just as it is with 1D data. The only difference is that there are more columns for the chemical shift and assignments (Figure 7-21). See page 57-1 for more information.
Plotting 2D Data 2D data may be plotted directly from 2D Viewer using the print icon on the Menu bar. From the Printer Tool, you can select a data destination, a printer, printer specication, paper size and orientation:
7-30
The default plot orientation is specied in the .delta_configure le in the user's home directory. The default 2D Viewer plot will include the contour data and the 1D data or projections.
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CHAPTER 8: PROCESSING RELAXATION DATA

INTRODUCTION
This chapter covers these topics: basic use of the T1 Analysis tool (page 8-1), collection of relaxation data (page 8-1), calculation of relaxation times (page 8-3), and plotting of relaxation data (page 8-9).
NMR relaxation data is calculated using the T1 Analysis Tool. To use the T1 Analysis tool: Select Viewers, then T1 Analyze, on the Delta Console menu bar. This tool can process T1 data (both inversion recovery and saturation recovery) and T2 data. The tool is designed to hold a two-dimensional data set, x_domain by time. By selecting different mouse cursor modes with the Cursor Tool, the user can perform different operations on the data le inside the geometry. Use Peak mode to select peaks. The mouse cursor will be set to Peak mode automatically when the T1 Analysis Tool is opened. Use Pick mode to take slices of the data for the T1 Analysis Tool. Use Zoom mode to get a closer look at a portion of the data.
COLLECTING RELAXATION DATA

Relaxation data must be collected using arrayed parameter. Arrayed parameters allow you to perform an experiment several times, collecting data for different values of the same parameters set up in advance. To set arrayed parameters from any section of the Experiment Tool: Click on a parameter label in the Experiment Tool Instrument window to bring up the tool for that parameter. Parameters can be set by either typing in the values directly or by entering: 1. An array of numbers. First select the dimension, then type the numbers into the white input box. Select the up arrow to sort the values in ascending order, select the down arrow to sort the values in descending order.
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Chapter 8: Processing Relaxation Data
2. A linear, logarithmic or exponential array. In these arrays, you provide the starting point, the stopping point, and the number of points in the array.
The following experiments may be used:
Table 8-1: Relaxation Experiment T1 inversion recovery T1 saturation recovery T2 double_pulse or double_pulse_dec double_pulse or double_pulse_dec cpmg
8-2
Collecting T1 Data
COLLECTING T1 DATA
Because the data set can only be collected in the x-y plane, we have to set up an array of tau values for the experiment to collect T1 data. Set up an array of tau values by using the Array Parameters tool.
PROCESSING RELAXATION DATA

Relaxation data should be processed using the standard the nD Processor tool to process the x dimension. The nD Processor can be automatically loaded when the experiment is nished by setting the experiment process function to process_ndimensional. Use the Slice option to load the rst slice from the relaxation data set to set the processing and phasing parameters. To load a 1D slice of data parallel to any dimension: Select the column for that domain by clicking on the domain button at the top of the processing list. The index value for the other domains will determine which slice is displayed.
Select the 1D Slice button: . A 1D Processor will start up and the slice will be loaded. If a processing list for that domain already exists, it will be copied to the 1D Processor and executed. After the 1D Processor opens, you may also create a processing list or make changes to an existing list in the 1D processor as you would for 1D data. When the processing list is correct, select Quit under the File menu to close the 1D Processor. The 1D Processor will close and the processing list will be transferred automatically to the nD processing list.
Click on Slate.
to process the le and save it to disc or
to save the data to a Data
CALCULATING RELAXATION TIMES

To start the T1 Analysis tool: Select Viewers then T1 Analyze from the Delta Console menu bar. A new window should appear. It will remain empty until you load an appropriate 2D data le, at which time it will resemble Figure 8-1.
8-3
Figure 8-1. T1 Analyze Tool
8-4
Calculating Relaxation Times
Select: To load a data set into the T1 Analysis Tool. Depending on whether the disk icon or the nger icon is depressed, the data le will be opened either from disk or from a geometry. When the data has been loaded, the top window will display the rst slice of the relaxation data set. Use the arrow buttons in the upper right corner to toggle between the rst and last spectrum in the data set. To generate the peak list from the 1D data. This is normally done on either the rst or last 1D data slice in the le. This step is not required to calculate a relaxation value. Adjust the Statistics (threshold, noise level, baseline) as necessary. This peak pick process can be repeated; therefore, it is best to start with a high threshold and work down. The peaks intensities and Y values should appear in the list box in the middle of the window. If the data set contains incorrect data points, you may need to choose a peak to see values. Remove them from the t by selecting the points in the intensity list, and clicking the Delete button. The points may be added back to the t with the Undelete button. To step one slice in the le in the negative/positive direction. To slice a le from a place you have picked.
Note: When this toggle button is depressed, the mouse cursor will change into Pick mode. Clicking the mouse anywhere within the geometry will update the value display window and the graph down below.
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Select: To slice a le from the nearest peak. Use search width input box on the upper right corner to set the range. Note: When this button is depressed, the mouse cursor will change into Peak mode. If Slice is selected, the value display window and the graph below will be updated only by clicking on a peak. Also, when this button is pressed, the data le must be peak picked before T1 analysis can be performed. Select Auto Analyze under the File menu or the peak pick icon to perform the peak picking.
To step one vector in the negative/positive direction.
To slice directly from the nearest peak.
Note: This choice is available only when the By Peak button is depressed. To take peaks nearest the slice point.
Note: This choice is available only when the By Peak button is depressed. To take peaks nearest the previously selected peak.
Note: This choice is available only when the By Peak button is depressed. Note: Slice, Track and Track Drift are radio buttons. Only one of these buttons can be on. To use peak height for intensity of point.
Note: Peak Height and Integral are radio buttons. When one is on, the other is off.
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Select: To use peak integral for intensity of point. Note: Integral may only be used for Track and Track Drift, not for Slice. To calculate peak intensities and Y values: 1. Select a region of interest using Zoom mode.
2. Use
to select the slice desired in the data set.
3. Select either
or
, then choose
, or
4. Then position the cursor anywhere in the data to select a position for calculation. Normally you will select a peak.
Note:
When and made only when you pick a peak.
are pressed, selections will be
is pressed, the data le has to be peak picked rst. to peak pick the data le.
5. Select Auto Analyze under the File menu or
6. The peak's intensities and Y values should appear in the list box in the middle of the window and be graphed below. 7. If the data set contains points which may be incorrect, you may remove them from the t by selecting the points in the intensity list, and clicking on .
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8. The points may be added back to the t with the
button.
Fitting Relaxation Data To t relaxation data: 1. First, select the desired tting model from the Curve Fit expression window whose buttons are outlined above. Delete To delete the currently selected value. Undelete To restore deleted values. Log data To display the natural log of normalized data. 2. Then, select to calculate the curve t. The data points and the calculated curve are displayed in the lower window. The coefcients for the current curve, standard deviation and Chi square value are displayed in the window next to the Curve Fit Expression window.
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Plotting Relaxation Data To plot relaxation data: Select File - Plot Curve or select to bring up additional toggle buttons used for plotting relaxation data. Select: Curve & Info - To plot the t curve with selected options. Peaks & Equations - To plot table of peaks and the t curve equation with all the coefcients and selected plot options. Vectors & Equations - To plot data points and equation of each vector with selected options. One Slice - To plot only the current vector. All Slices - To plot all selected vectors. Curve and Params - To format a curve with parameters. Multi-Column - For information laid out in blocks. Ascii Text - Tab-delimited elds of ASCII text, useful for processing on external spreadsheets. Vector Summary - To include the following parameters in the plot. Curve - To include a plot of the curve. Slice Point (x) - First X-value of the slice. X-value table - Table of X values of the slice. YI value table - Table of Y and I values of the slice. Curve t equation - Equation with coefcients. Standard deviation - To include the standard deviation value of the t curve in the plot. Chi square (X2) - To include the Chi square value of the t curve of the plot. Number of points - Number of data points in the slice. OK - Plot data with current state. Cancel - To cancel a plot and redisplay the data points and t curve in the lower window. Print - to set the destination of the current le as the plotter. A toggle that lets you select the destination. Note: This option is available only when Vectors & Equations and ASCII text are selected. Save File - To invoke the Save File Tool to save the current le while plotting. Note: This option is available only when Vectors & Equations and ASCII text are selected. True Data - To include the true data in the plot. Note: This option is available only when Curve & Info and Curve & Params are selected.
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Fitted Data - To include the tted data in the plot. Note: This option is available only when Curve & Info and Curve & Params are selected. File Menu Select File Open - To open a le from disk. Plot Curve - To plot relaxation data. Auto Analyze - To peak pick and integrate the current le. Close - To exit the tool. Ruler Menu Ruler - To select ruler type: Hertz, PPM, Percent, Points, or Seconds.
8-10

INTRODUCTION
Three dimensional NMR data, like two dimensional NMR data, is processed with the nD Processor Tool. The nD Processor displays one processing list column for each dimension. Each dimension is treated as a separate processing list. From any dimension, the user may examine a 1D spectrum along that dimension with a 1D Processor. This chapter will cover only the most basic 3D processing: loading 3D data, page 1 elements of 3D processing, page 2 3D Data Slate, page 8 3D Viewer, page 8 3D Slicer, page 12.
For a more detailed discussion of the nD Processor, refer to the DELTA Users Reference Guide. Before using the nD processor, you should become familiar with the 1D Processor and Data Slate tools.
LOADING 3D DATA INTO THE ND PROCESSOR

To invoke the nD Processor: Select in the Delta Console Tool Bar.
Or select Processors, then Process nD (^N) on the Delta Console menu bar to bring up the nD Processor (Figure 9-2). Then select File - Open or
A new window titled Open Data for Processing will appear (see Figure 9-1).
9-1
Current Directory Name List of Subdirectories List of Files File Info Name of Selected File
Figure 9-1. Open Data for Processing Window Browse the directories and select the three-dimensional le to be processed. Note: Multidimensional NMR data sets are all processed with the ND Processor. Each of the le's dimensions is processed separately and has its own processing list. The x dimension is processed rst; the y dimension next, etc.
ELEMENTS OF 3D PROCESSING
Domains DELTA treats each axis of an NMR data set as a domain. A domain has a nucleus type, spectral width, and processing parameters. An NMR data set may have only one major domain at a time. All other domains are called minor domains. In order to eliminate confusion about the order of t1, t2, and t3 evolution times in NMR data, DELTA uses the nomenclature x, y, z, , , , , to specify the domain. The x domain is always the dimension collected by the spectrometer receiver. The y dimension is always the next slower incrementing domain, z the next slower, and so forth. Processing can only occur on the major domain of a data set. The Transpose command interchanges the major and minor domains through a cyclical rotation. For n dimensional data, after n applications of Transpose, the major domain will be back to the starting location.
9-2
Figure 9-2. Empty 3D Processor Window Processing Lists Each domain of a multidimensional data set has a processing list (see Figure 9-2). The single list is broken up into multiple domain lists for ease of usage. These processing lists are similar to 1D processing lists. Each processing list column ends with the Transpose command that changes the major domain prior to going to the next domain. The Transpose command, like the Display/Phase command in the 1D processor, cannot be removed from the list.
To change the active domain: Select the active domain button at the top of each column. Only the processing list of the active domain may be edited. When the Process button is selected in the Processor tool, the entire processing list over all domains is executed. If you want to partially process a data set, leave the processing lists empty (except for [transpose]) for those domains not to be processed. Also, you may set the View to 2, 3, or 4 dimensions by selecting the numbers 2, 3, or 4 at the bottom left of the window. For Figure 9-1, the view was set to 3.
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Setting the X Domain List Each dimension of the 3D data will have a separate processing column. Normally, the domains are processed from left to right, i.e. X then Y then Z for a 3D data set. To recall processing lists from disk: Just as in 1D or 2D processing: use the Open List option under the File menu, or select on the Menu bar. To save a new list: Use the Save List option under the File menu or select To construct a 3D processing list: The 3D processing list may be constructed by selecting items from the Menu bar as was done for the 1D or 2D processing list. If the selected items appear in the wrong domain, change the selected domain by clicking with the mouse on the domain title button. The depressed appearance of the button indicates that the domain is selected. Setting the Y and Z Domain Lists Set the Y and Z domain processing column in the same way as the X column. .
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Creating a Processing List A processing list may be created either by copying from a list source, or by selecting elements for the list from the menu bar options. To process the list source and assemble the processing list for a selected dimension:
Select: To designate a disk le as source. Note: Use this icon with the Open List icon to load a data set or Processing list. To designate another Processing window as source. Note: Use this icon with the Open List icon to load a data set or Processing list. To load new data when the nD Processor is already open. (Alternatively, you may select File-Open File (Ô) from the menu bar.) To open a new nD le and remove the current processing list.
To open a processing list from the source determined by the source buttons. Note: If the source is set to from disk, the Open File Tool will appear. If the source is set to from another window, the mouse pointer will change to and the user must click on the window containing the desired processing list. To save the current processing list to disk. The Save File Tool will appear and the user will be prompted for a filename.
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Building and Manipulating Processing Lists To build a processing list: Select operators listed under the pull-down menus: 1. With the mouse, select a topic on the Menu Bar. 2. With the mouse button down, drag the mouse to highlight the desired option or command. 3. Release the mouse button and the option will appear in the selected processing list. Editing a Processing List To edit a processing list:
Select: To place the next processing item at the end of the current processing list. Even if a processing step is highlighted, the next selected item will be placed at the end. To insert the next processing item before the currently selected item in the list.
To change the selected (highlighted) item to the next item selected from the pull-down menu.
To cut the selected line from the processing list.
To paste a cut item at the selected location in the processing list. Note: Cut and Paste are local to the processing window. You cannot cut and paste items between different processing windows. To erase the contents of the selected processing list.
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To delete the currently selected (highlighted) item in the processing list. All items following the deleted item will be automatically renumbered. To copy entire lists from different dimensions of the nD Processor: 1. Select a domain by clicking on the name (i.e., X axis). 2. Click the Copy button. 3. Select the destination domain by clicking on the name (i.e., Y axis). Note: Each domain of an nD processing list always ends with the transpose statement. This statement always appears at the end of the list and cannot be removed. Its purpose is to cause the data to be phased and displayed in the window. Loading and Processing 1D Slices Often, it is convenient or desirable to look at a particular vector or 1D slice from a multidimensional data set during processing. Delta allows the user to extract any slice from the data set, process the slice as a 1D spectrum, and use the 1D processing list in multidimensional processing.
To load a 1D slice of data parallel to any dimension: Select the column for that domain by clicking on the domain button at the top of the processing list. The index value for the other domains will determine which slice is displayed.
Select the 1D Slice button:
A 1D Processor will start up and the slice will be loaded. If a processing list for that domain already exists, it will be copied to the 1D Processor and executed. After the 1D Processor opens, you may also create a processing list or make changes to an existing list in the 1D processor as you would for 1D data. When the processing list is correct, select Quit under the File menu to close the 1D Processor. The 1D Processor will close and the processing list will be transferred automatically to the nD processing list.
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3D DATA SLATE
To start the 3D Data Slate directly from an nD Processor:
Select . Data is automatically loaded after processing is completed. You may select additional views in the Data Slate using the menus. Help on the Data Slate offers additional information.
Figure 9-3. 3D Data Slate
3D VIEWER
The 3D Viewer (Figure 9-5) is based on the Data Slate. Help on the 3D viewer will give you additional information. To start a 3D Viewer directly from an nD Processor:
Select . Data is automatically loaded after processing is complete. The 3D Viewer can also be started from the Viewers menu in the Delta Console. When the 3D Viewer is started from the Viewers menu, it will appear empty until data is loaded.
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3D Viewer
The 3D Viewer is a specialized tool for displaying 3D data. As shown in Figure 9-5, its unique layout is designed for optimum analysis of 3D data. The 3D data is displayed as a cube in the upper right quadrant of the window; the other three quadrants are reserved for 2D projections. The Project menu will allow you to Toggle between 2D projections and slices (select Toggle Proj/Slice under Project in the 3D Data Viewer menu bar). Keep in mind that these are actually separate data geometries which are alternately displayed in a single display area. Each 2D area has associated 1D projection and slice areas along the bottom. When the 3D Viewer is rst started, the areas reserved for slices are displayed as the projection data until the Pick Cursor is selected, and data slices are chosen. The 1D and 2D data labels are always in the base units of the 3D data le. If you change the display labels with the Rulers menu, the le units displayed with the slices are unaffected.
2D Display Area 3D Display Area
Figure 9-4. 3D Viewer Right Mouse Button Mode Selection Menus
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Figure 9-5. 3D Viewer Three-Dimensional Display Modes Three-dimensional data may be viewed in several display modes. The display mode is selected by pressing the right mouse button on the data and selecting a mode from the options menu. Depending on the Display Area dimension, the Selection Menu will vary (see Figure 9-4). 3D Display Modes resemble 2D Display Modes. In addition, the third dimension allows for rotation, translation, and in/out zooming when the Display Mode is a 3D representation.
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3D Viewer
Figure 9-6. 3D Viewer - Slices
Figure 9-7. 3D Viewer - Zoomed
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Loading 3D Data To start the 3D Viewer:
Select . A new window called Open File will appear (Figure 9-1 on page 9-2). From the Open File Tool, select the le to be viewed.
If the 3D viewer is already running, new data is loaded using the Open Folder icon or the Open File (Ô) located under the File menu in the Menu bar. Data can also be graphically loaded from another window into 3D viewer using the Finger icon .
3D SLICER
The 3D Slicer Tool is a specialized tool for displaying 3D data. As shown in Figure 9-8, a unique layout is designed for slice analysis of 3D data. The 3D data is displayed as a cube in the bottom right of the window and a space is reserved for 2D and 1D projections or slices. When the 3D Slicer is rst started, the areas reserved for 2D and 1D are displayed as projection data. The 3D Slicer (Figure 9-8) is also based on the Data Slate. The 3D Slicer can be started from the Viewers menu in the Delta Console. When started from the Viewers menu, it will appear empty until data is loaded. For more information, consult help on this tool.
Figure 9-8. 3D Slicer with Overlaid Spears
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3D Slice Plotter
Multidimensional geometry options For 2- and multidimensional processing, in mesh and surface modes, these geometry options are added to the options menu that you call from the data geometry using the right mouse cursor: Full Spatial Reset [Shift Home] Rotate +/- X, Y or Z [Dwn, Up, Lft, Rgt, ShLft, Sh-Rgt] Translate +/- X, Y or Z [Cntl-Dwn,Up,Lft,Rgt, Sh-Up,Sh-Dwn] To zoom out to see full data set, keeping the present perspective. To rotate the data geometry left, right or in the 3rd dimension.
To move the data set left, right, or in the 3rd dimension.
3D SLICE PLOTTER
Use the Slice Plotter to plot 2D slices of 3D data les. The slices that are plotted are taken at coordinates where peaks exist in a le.
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To invoke the Slice Plotter: Select the 3D Slice Plotter command found in the Tools menu of the Delta Console. Select View Peaks to view a 1D projection:
Select Contour Levels 2D slices:
to set the contour levels for plotting
Geometry Display Contour Levels
To select Peaks and Contour Levels: The slice you print has the same contour levels as the 3D overview geometry. Therefore, you may want to add or delete peaks and change the contour levels before you begin to print slices. Select from three different orientations:
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3D Slice Plotter
To summarize: when Slice Plotter is brought up, it calculates an XY projection (a projection along the X and Y axes), an XZ projection, and a YZ projection. Each projection is peak picked, and the peaks are displayed. When the plot button is clicked on, a slice is taken from the le at the coordinate of each peak in the displayed dimension. The slice is then queued to the default plotter. The plot selector determines the number of slices that will be plotted on one page.
If the single page button is selected, then the plots will be queued with only one slice per page. If the multi-page button is selected, then six slices will be plotted on each page. Finally, use the Plot Slices button to queue slices to the printer. For further information, consult the treatment of this tool in Delta online Help or in the Users Reference Guide. Cursor Tool
Mode Operations Tab Cursor Tool functions for 3D are similar to those used in the 1D or 2D display mode. Start the Cursor Tool by selecting the Tab . Select a Mode by scrolling the list, then select an operation button. The mouse cursor will change shape based on the active operation.
Place the Cursor Tool in Zoom mode to zoom in on and rotate data. Select: to zoom in on the data, In either the 2D or 1D projections/slices, draw a box around the data you would like expanded and it will be enlarged. In the 3D box you will see a white box drawn around the data. This is not expanded but the view of it has been brought nearer. To zoom out, press the backspace key to zoom out incrementally; press the home key to return to the original. to rotate the data around various axes. Drag the mouse horizontally to rotate the data around the y-axis; vertically to rotate the data around the x-axis; diagonally, to rotate the data around the z-axis.
to use the crosshair Cursor. The crosshair Cursor operation differs slightly in 3D displays. You may create and delete 3-dimensional cursors as you do in 1 and 2D, and they will be linked to the lower dimension display areas. You can also move this cursor in 3-dimensional space. The crosshair button (in zoom and in cursor modes) lets you center the crosshair in spatial or mesh mode; a 3-dimensional crosshair is placed in the display area when you click the right mouse button while holding down the SHIFT key. The next mouse function (move, select, or create) will place the appropriate cursor lines at this center mark. The arrow keys (along with the SHIFT key) allows you to move the 3dimensional center crosshair along any of the 3 axes.
The crosshair cursor and the pick cursor cursor functions in the 3D display area.
are the most useful
Pick Cursor The 3D Pick position cursor in Pick mode of the Cursor tool is like the 2D version, except that there are three intersecting planes that dene the three 2D contour areas. These planes are linked to the lower dimension display areas, and the index mark on the lower dimension axes indicates their locations. If you change the Pick cursors on the lower dimension displays, the 3D intersecting planes will track. However, the 3dimensional center crosshair will not be updated, so that when you select the Pick cursor in the 3D display area again all the Pick cursors will be reset to those coordinates. You can move the 3-dimensional center crosshair along any of the 3 axes in the Pick cursor mode.
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3D Slice Plotter
Use the Pick Position button to get reference values in a multidimensional data geometry: Move the blue crosshair cursor in the geometry and select x, y and z reference values by clicking on the desired position. Note: In multidimensional geometries, select a reference point by moving this blue cross not only up and down, left and right, but also into depth.
Note: The arrow, in multidimensional geometries, indicates the presence of a peak: red indicates negative, green positive. arrow blue 3D crosshair
Figure 9-9. 3D View Control
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Rotating and Translating 3D Data For 3D data, the mouse does not have the axes of freedom to adequately describe 3D motion. The arrow keys together with the Shift and Control keys give the necessary additional rotation and translation functions. The optional Spaceball, however, allows for 6 axes of freedom and can be used to manipulate 3D data. To rotate or translate data using keyboard keys: To rotate the 3D image along the vertical axis (-X or +X), you can use the Left or Right arrow keys. To rotate the 3D image along the horizontal axis (+Y or -Y), you can use the Up or Down arrow keys. To rotate along the axis perpendicular to the display (-Z or +Z), you can use SHIFT Left or Right arrow keys. The SHIFT Up arrow will translate the image back along the Z axis (into the plane of the screen). The SHIFT Down arrow will move the image out along the Z axis (out from the plane of the screen). The CTRL Left or Right arrow keys will translate the image left or right along the X axis, while the CTRL Up or Down arrow keys will translate the image vertically along the Y axis. Home will reset the 3D spatial view.
Slice and Projection Areas When 3D viewer is initialized, three separate areas are reserved for each axis. All of these areas are initialized with 2D data projections. The Display option on the Menu bar allows the user to turn these areas on or off independently. The area closest to the 3D data is called the Slice area and is updated each time a Pick is made by the mouse. The outer area, called the Projection, is updated when a projection is done. 3D Peak Pick and Data Reduction Analogous to 2D processing, 3D data peak picking and integration are performed with the Peak cursor. To view peaks: Select Peak Pick in the geometry pop up menu. If the peaks do not match the data, it is because you have not selected the Peak Pick icon rst. Simply hit the Peak Pick icon to recalculate and refresh the display. The peaks will be displayed as octagons with the peak width in each direction represented by a pair of crossed lines.
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CHAPTER 10: EXPERIMENT TOOL AND ECLIPSE EXPERIMENT PROGRAMMING

INTRODUCTION
This chapter describes the Eclipse Experiment programming language and spectrometer features, offering details on: loading experiments, page 10-2 syntax and operators, page 10-7 the Header section, page 10-17 the Instrument section, page 10-23 the Acquisition section, page 10-26 the Pulse section, page 10-29 submitting experiments, page 10-32. arrayed parameters, page 10-48
This chapter is intended for the NMR system manager and advanced NMR operators who need to customize or write experiments for the Eclipse NMR. The reader should be familiar with the operation of the Eclipse NMR and a UNIX le editor. This manual describes certain features and options of the spectrometer that, when used incorrectly, could damage certain NMR probes. You are urged to read and understand all of the material before making modications to any experiments. If you have any doubts about making changes to an experiment, please contact either the JEOL NMR Applications department or the JEOL NMR Service department before making the modications.
DEFINITION
The Eclipse NMR spectrometers use the concept of an experiment to control the spectrometer. An experiment contains: Header parameters - filename, identification code, sample tracking code, operator comments, post-acquisition processing, etc. Instrument parameters - physical hardware control parameters, i.e., temperature, receiver gain, audio filters, etc. Acquisition conditions - NMR frequencies and offsets, data points, scans, etc. Pulse sequence - pulse widths and associated timing parameters.
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Chapter 10: Experiment Tool and Eclipse Experiment Programming
An experiment contains all of the information needed to create an NMR data set. The experiment is also stored inside the Eclipse data set and may be retrieved from an Eclipse data set using the Experiment Tool, the loading and running of which is described in this chapter, in online help on the Experiment tool, and in the Delta Tutorial (page 4-1). The experiment pulse sequence and default spectrometer parameters begin as ASCII les in the user's experiment subdirectory or the global experiment directory. The Eclipse experiments are organized in a local user subdirectory ~/delta/experiment and a global experiment directory /usr/delta/global/experiment. Pulse Sequences Experiments are used to generate pulse sequences. The advantage of storing the parameters with the pulse sequence is that reasonable default values for the experiment are always set. Parameter Files Experiments are also used as parameter les. The default values in an experiment can function as a parameter set; if desired, the user may be kept from changing the defaults.
LOADING EXPERIMENTS
Spectrometer Control Tool The Spectrometer Control Tool is shown in Figure 10-1. To load an experiment, the Spectrometer Control must have a connection to or be monitoring an Eclipse spectrometer. To load an experiment: 1. Select the Spectrometer Control Tool icon . The spectrometer control tool will appear (Figure 10-1). 2. Connect to an active spectrometer. The spectrometer uploads the spectrometer hardware parameters, parameter ranges and standard values to Delta. The experiment tool uses this information to set up experiments.
10-2
Loading Experiments
Figure 10-1. Spectrometer Control Tool after Connection 3. Then select the Expmnt button from the row at the bottom of this window to activate the Experiment Tool. When the Expmnt button is clicked, the standard Open File window will appear (Figure 10-2).
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Figure 10-2. Open Experiment File Tool See Open Data Tool on page 37-1 for further information on this tool. 4. Select the desired experiment from the list of les in either the 'home' (local) experiment directory, or the 'global' (system) experiment directory. The default locations for these directories are specied in the .delta_configure le. Note: A new experiment can also be loaded into an existing experiment window.
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Experiment Tool
EXPERIMENT TOOL
The Experiment Tool is shown in Figure 10-3.
Figure 10-3. Experiment Tool Loading Experiments from Other Data Sets The Experiment Tool has the following icons and buttons. Their use is described here: Table 10-1: Experiment Tool Icons Select: To move to different locations in the experiment window.
10-5
Table 10-1: Experiment Tool Icons Submit To submit the experiment to the queue. To select a le and apply the X dimension features from the le you selected. This sets the sweep width and offset for the domain. The focus is determined by the Source icon status and from either another data le (disk) or another geometry window (nger). To select a le and apply the Y dimension features from the le you selected. To select a le and apply the Z dimension features from the le you selected. Experiment Source Icons To designate an experiment text le (default) as data source. When the open le icon is selected, an Open File window appears.
To designate a geometry or data window as the source of an experiment. Because the experiment is stored with the data, the experiment may be recovered from another displayed data set using this mode. To designate a data le on disk as the source of an experiment. Because the experiment is stored with the data, the experiment may be recovered from a data le using this mode. Open File Icons To open a new experiment into the existing experiment window. All experiment parameters are initialized to the values of the new experiment.
To open a new experiment into the existing experiment window. Any experiment parameters with the same name keep their current values.
Save Experiment Icon
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Syntax and Operators
Table 10-1: Experiment Tool Icons To save the current experiment to disk. The Save File window will appear and a le name may be entered. The experiment le is an ASCII le interpreted by the Eclipse Experiment Tool. However, any include les or macros are expanded. Therefore, the text of the saved experiment may look different from the starting experiment. Match Icon To copy the parameter values from another experiment and place them in the current window. It compares only the names and values of the parameters, not the pulse sequence. It will not add new parameters to the current experiment - only update matching parameters. Help Icons To bring up on-line help on the current experiment, if it is available.
To bring up on-line help for the experiment tool.
SYNTAX AND OPERATORS

The experiment le is an ASCII le interpreted by the Eclipse Experiment Tool. The Delta program constructs the experiment window as the experiment is loaded. Control of all experiment parameters and their initial values are determined by the syntax inside the experiment le. Experiments are interpreted as programs, and as such the syntax of the ASCII le must be followed. The following general rules apply to all experiments. Syntax Rules Each command must be terminated with a semi-colon ; The double dash -- indicates the beginning of a comment string. All characters after the -- are ignored. The Pulse section of the experiment must have a begin statement.
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Operators Addition (+) Performs addition of the operands. Subtraction (-) Performs subtraction of the operands. Multiplication (*) Performs multiplication of the operands. Division (/) Performs division of the operands. Concatenate (||) Combines or concatenates two or more sets. For example: a = {0,0,180,180}; b = {90,90,270,270}; phase_1 = a||b; -- phase_1 is {0,0,180,180,90,90,270,270} Round Rounds the input value to the nearest integer. The input may be a variable or expression. Assignment (=) The assignment statement is used to equate and initialize variables and parameters. Statements using the = symbol are not displayed in the Experiment Tool, and thus their values are not user observable or modifiable. The = symbol is also used as a Boolean operator in if-then-else clauses. Assignment with modiable display (=>) The modifiable assignment statement is identical to the assignment statement except the result is displayed in the Experiment Tool and you can adjust the value. The user input window takes on different forms depending on the type of parameter: input box
constrained input
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list box
select enumeration
Assignment with display only (=?) The assignment with display statement is identical to the assignment statement except the value is only displayed and cannot be changed by the user. These items are shown as labels in the experiment tool. label
Examples of assignments Strings

filename => nmr_spectrum; x_domain => 'Carbon13';
Numeric values (integer or real)

scans => 8; define relaxation_delay => 3.0`[sec];
Expressions
define x_pulse => x90/2;
Enumerations
define evolution => 1/4J, (1/4J,2/4J,3/4J); define multiplicity => CH, (CH, CH2, CH3);
Ranges
define x_angle => 45`[deg], 1`[deg] -> 360`[deg] :1`[deg]; define dept_pulse => 45`[deg],45`[deg]->135`[deg]:45`[deg];
Boolean
auto_gain => false;
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Current parameter value reference (#) The # symbol is used to reference a current hardware parameter value. For example, if a sample in chloroform-d is locked and shimmed, the lock solvent was already input in the Sample Tool. When the Experiment Tool is initialized, the solvent value in the experiment should be set to chloroform-d. This automatic substitution behavior is achieved using the syntax:
solvent => #;
The # symbol automatically references the hardware parameter of the same name. Experiment Parameters The experiments have several pre-defined parameters. These parameters are initialized using assignment statements. Not all of these parameters are used in all experiments. Each predefined experiment parameter -- i.e. every parameter thats in the header, acquisition or pulse section -- can optionally be given user-defined defaults in the .delta_configure file. These predefined experiment parameters cannot be changed with the Preferences Tool. Each parameter can be given its default value in the file by preceeding the parameter name with "experiment .". For example, to set a parameter for the scan parameter, you might write "experiment .scan = 16". The only exception to this rule is the sample_id. If you write "experiment .sample_id = time", then the current system time in tenths of seconds will be used as the sample_id time in the experiment.
Table 10-2: Experiment Header Parameter Denitions Header Section comment Default -Parameter Control Description Experiment comment, placed in the content eld of the collected le. A string that lists the potential target nodes that will receive the completed experiment. Only one system will actually get the experiment. An * in the list indicates the submitting workstation. The default lename is provided in the following format: YYYYMMDD_nD_sample_id_num.num.
destination
lename
--
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Table 10-2: Experiment Header Parameter Denitions Header Section lter_limit lter_start lter_stop init_group Default 0 0 0 0 Parameter Control Description Sets the oversampling factor for digital ltering. Sets the starting axial position for digital ltering. Sets the ending axial position for digital ltering. Determines which init_group of pre and post instrument conditions are used. If omitted, then the experiment domains are appended. It is used to help select the correct probe for the experiment. The name of the Percival macro or program invoked after collection. The resulting lename is appended to the end of this line and it is spawned on the workstation that received the completed experiment. Used for sample tracking and automation queue management. If omitted, a unique number is generated. Changer slot on which to run the experiment. Number indicating the percentage of the max value used as the highest point to be searched for a 'signal' peak. Omits the region around the center of the spectrum and the region about the largest peak. Starting point of the region used to determine the spectral noise. Ending point of the region used to determine the spectral noise. Number indicating the desired signal/noise ratio of the data. The experiment will terminate when this value is reached. A set value of 0 for the sn_ratio deactivates the calculation. Starting point of the region used to determine the signal intensity. Ending point of the region used to determine the signal intensity.
probe_attr
--
process
--
sample_id slot
-0
sn_border
100
sn_noise_start sn_noise_stop
0 0
sn_ratio
sn_signal_start sn_signal_stop
0 0
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Table 10-2: Experiment Header Parameter Denitions Header Section sn_skip Default 10 Parameter Control Description Number of scans to skip before starting to check for signal to noise. A string in the format DD-MTH-YYYY HH:MM:SS that indicates at what time (instrument time) the job should be started.
start_time
current
Table 10-3: Experiment Acquisition Parameter Denitions Acquisition Section mod_return Default Parameter Control Description Number of vectors skipped between vectors returned to the workstation. Also determines how often signal-tonoise ratio should be sampled. Number of scans to collect. 0 results in 32K scans. Negative numbers result in outer scans on 2-dimensional acquisitions. If the experiment is 1-dimensional, the outer scans are converted to normal scans and the maximum value is 2
30
scans
(1,073,741,824).
CHAN is an RF channel (IRR,TRI) Sets a non-observed channel to a domain. Used when an experiment requires a decoupling frequency, but the decoupling frequency is not used as a multidimensional domain. Sets a non-observed channel to a specied frequency MHz. An offset from the base frequency of the CHAN_domain or CHAN_freq in Hz or ppm. n is a domain (x,y,z,a,b,c,d,e) n_points n_prescans 1 0 Number of points to collect in each dimension. Number of prescans before starting to collect.
CHAN_domain
CHAN_freq CHAN_offset
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Table 10-3: Experiment Acquisition Parameter Denitions Acquisition Section n_sweep n_domain n_freq n_offset Default Parameter Control Description Sweep width each dimension in Hz or ppm. This will be corrected (adjusted) at run-time for actual NMR ADC dwell period. String indicating the desired nucleus for the domain. Overrides the n_domain by forcing a specied MHz value. An offset from the base frequency or domain in ppm or Hz.
Table 10-4: Experiment Pulse Parameter Denitions Pulse Section Default Parameter Control Description A string that allows various special module features to be controlled (see Pulse section description). the module_cong line in the experiment must specify the "lock_switch" option. This causes the pulse compiler to actually congure the head_amp to use the lock switch device. Indicates the total run time of the job. This is used for scheduling. Note: a job of time 0 is assumed to take innite time.
module_cong
total_time
Dene statement The dene statement is used to create new variable names for use inside the experiment. A variable must be initialized with an assignment statement when it is dened. For example:
define relaxation_delay => 1`[sec];
Strings String values must be enclosed in matching quotes, either matching single quotes ` ` or matching double quotes .
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Units The Delta software uses unit types throughout. The unit symbol is the single backquote `. The unit type is enclosed in brackets [ ]. Consult the Delta Programmers Reference Manual for more information on units. Align The align statement takes all statements between the align and end align, and breaks the total time into unique discrete times according to the modier. The align statement takes three modiers - leading, center, and trailing. The order of the times is not important. The precision of the resulting pulses is limited by the pulser hardware. The align statement is most useful for centering pulses of different lengths from multiple channels, i.e. simultaneous 180 pulses from observe and decoupler channels. For example: align center x_pulse*2, (obs.gate, obs.phs.phase_1); y_pulse*2, (irr.gate, irr.phs.phase_2); end align;
o
align trailing x_pulse, (obs.gate, obs.phs.phase_4); y_pulse, (irr.gate, irr.phs.phase_5); end align;
Macro Macro statements are similar to subroutines. Macros must be dened before they are used and they may be loaded from include les. The syntax is macro name (optional input variables) is .... end name;
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For example: macro mlev (pulse_90, phase) is .... end mlev; Note that there is no ; after the is statement. The input variable names in a macro are self-declaring and do not need to be dened separately. Variables are passed into a macro in the order listed when the macro is called. Take care to ensure that the variable order matches the macro declaration. To use a macro from inside a pulse sequence, the syntax is: macro_name (optional variables); For example: mlev (x_pulse, phase_lock); Loop The pulse sequences have looping capability. The maximum value for a loop is 4095. Loops may be nested up to 7 levels. loop value times .... end loop; Note that there is no ; after the times statement. For example: define loop_number = 4; loop loop_number times .... end loop; Begin The beginning of a pulse sequence is marked with a begin statement. All statements following the begin are interpreted as time states in the pulser. The pulse sequence terminates with an end pulse; statement. Conditional if-then-else statements In the experiment le, if-then-else logic is supported. The if-statements can be used only in dene statements and assignment expressions. The syntax is
10-15
define variable = if condition then expressions else other expressions; If-then-else statements may be nested: if condition_1 then expression_1 if condition_2 then expression_2 else other_action_2 else other_action_1 The Eclipse spectrometer does not support runtime conditional if statements in the pulse sequence.
INCLUDE FILES
The include statement, "include filename, lets an experiment load additional les into an experiment at compile time. Include les are incorporated and expanded in the experiment just as if text were included in the original le. The best candidates for include les are commonly used sections of experiments or extensive macro functions used in many different experiments. The syntax for an include le is: include filename; User Include Files Users may have their own private include les in their own experiments. Standard Include Files Standard Include Files The standard global include les for experiments are listed in Appendix A. std_header std_instrument std_dec_instrument std_solid_instrument std_acquisition std_2d_acquisition std_3d_acquisition
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Header Section
All user written experiments should include these files for compatibility. Include les are expanded in the experiment when it is read into the Experiment Tool. Include les are useful for standardizing the format of experiments and adding global modications to the experiments. All of the JEOL-distributed experiments reference the standard include files. User-written experiments should reference the standard include les for compatibility. Set up properly, one could use include les to change an experiment parameter in all the experiments on a spectrometer. For example, to add the slot parameter for an autosample changer, the System Manager would change the std_header le, which would immediately add the header ag to all experiments.
HEADER SECTION
The Header section includes the basic attributes of the sample, data collection, and data storage. A typical Header is shown in Figure 10-4. The Header is composed of list boxes for string names and radio buttons for feature control.
Figure 10-4. Experiment Tool Header lename The filename is the string indicating the name of the le containing the data after
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collection. In this eld, enter a lename. If a le of the same name already exists, a new le with a unique version number will be created, so the existing le will not be overwritten. Do not use slashes, brackets, dashes or spaces in the lename. Note: the lename does not include the version number. The Delta program appends the version number automatically based on how many other les of the same name exist. If a lename is left blank, the software will create a unique name composed from the data and time when the acquisition nishes. sample_id The sample_id is a unique string which identies the particular sample. In this eld, assign a sample name to differentiate among measurement samples. If the sample id is left blank, the software will assign a unique number. Many features of the spectrometer queue use the sample_id. The software depends on the sample_id in making assumptions about queue control and automation. In the queue, if two experiments have the same sample_id, the software assumes the correct sample is already in the magnet and will not load, lock, and shim for the second experiment. If multiple experiments are run on the same sample, the sample id should be the same. comment The comment is a free format eld in which you may enter information relative to the sample or experiment. No special syntactical rules apply to this eld. process The process eld is the name or command of the program or macro to be invoked when data collection is completed. The standard process lists are automatically set. If it is blank, the data is simply written to disk. Table 10-5: Header Process Information Options process_oned process_ndimensional Invokes the process_oned program. Checks the data and invokes process_oned for 1-D data and process_ndimensional for all other data. Invokes the 'process.list' name processing list in the global process_list directory. Invokes the 'process.list' name processing list in the user's local process_list directory.
process_global 'process.list': process_local 'process.list':
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Header Section
Autosample Changer slot On systems with an automatic sample changer, the slot parameter determines the location of the sample for that particular experiment. On systems equipped with an automatic sample changer, add the following line to the std_header le. This will add slot control to all experiments. slot => 0; Header Flags Header ags control (on/off) various features in the spectrometer and acquisition conditions. Only some of the header ags are shown to the user; others are set in the std_header include le. If the ag is not initialized, the default values apply. Header ags demonstrate the use of the std_header include le to quickly customize all the experiments for a site. To remove, add, or change the default value of a Header Flag, make the change in the std_header le and all of the global experiments will reect the change. Experiment Flags Legend T = True F = False S = String I = Integer Table 10-6: Header Flags Name allow_copy auto_dwell Default T T Action when the Flag is set to TRUE Enables copy of data during acquisition. When set to TRUE, the acquisition dead time and delay will be automatically calculated; when FALSE, the user must supply these values. Causes the acquisition to digitally lter the data automatically within the maximum sampling rate. Causes the recvr_gain to be automatically set before the data is collected.
auto_lter
auto_gain
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Table 10-6: Header Flags Name Default Action when the Flag is set to TRUE Runs these machine les that contain instrument parameters and that are found in the /eclipse directory on the acquisition computer: automatic F machine.defaults for Experiment Initialization. machine.pre_exp for Data Collection, and machine.post_exp for Experiment Finalization. Creates an output le for the collection. The vector ag is respected. Uploads data to a workstation dened in the string. This workstation must have Delta installed on it, and you must have an account on it. Causes the sample to be ejected upon completion of the experiment. Digital lter limit based on FILTER_LIMIT set in machine.config. Start point in [ppm] or [Hz] for digital ltering. Stop point in [ppm] or [Hz] for digital ltering. Uses inverse Chebychev instead of elliptical Jacobian digital lter. Sets the autotune to be done regardless of previously tuned domain. When FALSE, if the domains match, then probe is not retuned. In the case of a manually tuned probe, the spectrometer is set to tune mode and the user must tune the probe and acknowledge it on the screen. Forces EVERY vector to be returned for the vector view regardless of timing constraints. When FALSE, if the last vector has not nished the process and display functions before another acquisition begins, that vector is skipped. Causes the queue to be 'held for another job.
create_le
destination
eject lter_limit lter_start lter_stop lter_wide
F I S S F
force_tune
force_vector
hold
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Header Section
Table 10-6: Header Flags Name init_group Default I Action when the Flag is set to TRUE Calls specic machine.defaultsx, machine.pre_expx machine.post_expx (x = 0 -> 9) Makes this job part of a collection of jobs that will be scheduled together. The pre and post les will only be run before the rst and after the last le in the group. Acquires and downloads a pulse program. If FALSE, delay for total_time and then stop. Don't download the pulse program. Causes the shims to be loaded for the experiment. Aborts the experiment if the lock is lost. Waits for probe and/or sample checks. Causes the last arrayed dimension to be returned in separate les instead of a virtual dimension nD le. When TRUE, the experiment will not run until the experiments owner no longer owns the queue. Runs the pre and post instrument initialization les. Executes an experiment only if string matches any value from the rst line of the probe le. On autotune probes, use the quick tune feature instead of full tune. Repeats the experiment until told to stop. Resubmits the experiment when 'ok' is pressed until aborted. Rounds the point values in dimensions greater than 1 to the next greater or equal power of 2. The x_domain is always rounded. If an experiment that collects a le is aborted, saves and uploads the le instead of deleting it. Invokes the special sawtooth mode.
job_group
load_pulser load_shims lock_check match multi_le not_owned pre_post probe_attr quick_tune repeat resubmit
T F F T F F T S F F F
round_points
save_aborted sawtooth
F F
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Table 10-6: Header Flags Name Default Action when the Flag is set to TRUE When set to TRUE in the experiment header, the temperature control is turned ON, the instrument waits for the value of TEMP_SET (sample temperature setpoint) to be reached and settled before beginning the experiment. If set to TRUE with the temperature control OFF, a warning message is given and the experiment proceeds. The temperature settling process may take up to 10 minutes. A warning message is given and the experiment proceeds regardless of the outcome of that process. I I I I I I I I S Sample changer position. Maximum s/n value for the data. Start point for noise used in s/n calculations (ppm/Hz). Stop point for noise used in s/n calculations (ppm/Hz). Value of s/n ratio when achieved will terminate the experiment. Set to zero to turn off s/n checking. Start point for signal used in s/n calculations (ppm/Hz). Stop point for signal used in s/n calculations (ppm/Hz). Don't stop experiment for s/n ratio below this value. Starts experiment at a specied time. The time clock is the acquisition system not the workstation. Syntax: ddMMM-YYYY hh:mm:ss (13-FEB-1997 12:50:45) Sends back real-time vectors for viewing (see force_vector).
settle_vt
slot sn_border sn_noise_start sn_noise_stop sn_ratio sn_signal_start sn_signal_stop sn_skip start_time
vector Header Parameters
In addition to the Header Flags, there are Header Parameters that also control various features and acquisition conditions. Only some of the Header Parameters are shown to the user; others are set in the std_header include le. If the parameter is not initialized, the default values apply. (See Table 10-2 for a complete listing of these parameters.)
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Instrument Section
Adding Header Flags and Parameters Dynamically To add Header ags and parameters to the Experiment Tool: Click on the name Header in the Experiment Tool window. A new window will appear on the screen (Figure 10-5). Select the header elds you want to include, clicking Add after each selection. When you are nished, click Done and the Experiment Tool will redraw to show the new elds. 5. For example, you may want to control the use of the Copy function, disallowing copy, by default, for automation experiments. To do this, select the allow_copy experiment header parameter on the header parameter list that pops up when you select the Header title in the header window. Make sure the check box is unchecked and press the Add button, then press the Done button. 1. 2. 3. 4.
Figure 10-5. Adding Header Fields
INSTRUMENT SECTION
The Instrument Section (Figure 10-6) contains all of the spectrometer hardware parameters. Hardware parameters are those that have a direct correspondence to physical hardware controls or attributes. The full list of parameters is in Appendix B: Instrument Parameters. All of the hardware parameters can be viewed and changed using the
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Parameter Viewer on the Spectrometer Control Tool. The hardware parameters are all pre-dened and may be used in assignments and expressions. Only the most commonly used parameters will be discussed here.
Figure 10-6. Experiment Tool Instrument Section Solvent The solvent is the deuterated lock solvent, which you normally set in the Sample Tool. Otherwise, you may select one from this list. The solvent parameter is used for setting the lock offset frequency, lock power and lock gain. The default values for each solvent are in the solvent.def le. If the solvent parameter is not set correctly, the auto-reference values may be incorrect. Receiver gain (recvr_gain) The receiver gain determines the amplier gain on the receiver. It should be optimized manually or by using the auto_gain header ag. Normally the receiver gain is adjusted so one scan lls 50% to 80% of the ADC range. Running the ADC at a lower receiver gain will only slightly affect the dynamic range of the data. Over-running the ADC by using too large a gain will cause the FID signal to be clipped. If the automatic gain setting is not used, set the receiver gain.
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Instrument Section
Temperature control (temp_state and temp_set) Temperature control may be performed either from the Sample Tool, or from individual experiments. If the temperature settings or modes from the Sample Tool and the Experiment Tool contradict, the Experiment Tool has priority. For example, if the NMR o sample has stabilized at 50 C, then an experiment is submitted with the TEMP o STATE OFF, or, if TEMP_SET = 70 C, the spectrometer will adjust to the new conditions before running the experiment. If the experiment does not change the temperature settings, i.e. neither the TEMP_STATE or TEMP_SET are specied either visible or hidden, the experiment will continue with the current settings. The order of the parameters in the Experiment le is important. The TEMP_SET value should precede the TEMP_STATE. Thus the value in the set temperature register should be initialized before the temperature control command is issued. Table 10-7: Temperature Parameter List Parameter TEMP_STATE TEMP_GET TEMP_SET TEMP_COMP TEMP_DELAY TEMP_LIMIT_HI TEMP_LIMIT_LO Function of the Temperature Parameter Variable temperature state ON or OFF Current temperature Desired nal temperature Compensation value - usually 0 Time delay to wait for sample equilibration after the variable temperature unit has reached the target temperature High temperature limit for the probe in the *.probe le Low temperature limit for the probe in the *.probe le
Audio lter type (lter_mode) The Eclipse spectrometer supports two type of analog audio lters, Butterworth and Bessel. For most spectroscopy they can be used interchangeably. Butterworth lters will produce a slightly larger rst-order phase error near the spectral edge. Bessel lters more easily adjust a dish effect or DC offset in the baseline.
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Adding Instrument Parameters Dynamically To add an instrument parameter to the Experiment Tool: 1. 2. 3. 4. Click on the Instrument title in the Experiment Tool window. A new window will appear on the screen (Figure 10-7). Select the instrument elds you want to include, and click Add. When you are nished, click Done and the Experiment Tool will redraw to show the new parameters.
Figure 10-7. Adding Instrument Parameters
ACQUISITION SECTION
The Acquisition section of an experiment (Figure 10-8) most closely resembles a traditional parameter le. The acquisition section contains information about the NMR frequencies, sweep widths, data points, etc.
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Acquisition Section
Figure 10-8. Experiment Tool Acquisition Section Domains Eclipse experiments use the concept of a domain. A domain is the NMR nucleus or frequency associated with the data sampling in a particular dimension. Usually the name of the nuclear species is used instead of the frequency, thus removing the instrument/ magnetic eld dependence from the experiment. The instrument frequency (MHz) for a domain is calculated from the eld strength in Tesla (in the machine.config le) and the gyromagnetic ratio (in the gamma.def le). Domain order progresses from x to e in the order (x,y,z,a,b,c,d,e). x Domain The x_domain is the observed NMR signal which is digitized in the A/D converter. You may select the nucleus to be observed. y and Higher Domains Domains labeled y or higher (y,z,a,b,c,d,e) are higher dimensionality nuclei, indirectly observed by the experiment. They can be the same as the x_domain as in a COSY or different as in a CH correlation. Spectral Offset The domain species the particular nuclear base frequency. In this eld, you may set the observation center frequency (ppm). Often it is necessary to shift the spectral center to
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observe another part of the spectrum or to optimize the spectral width for a multidimensional experiment. The spectral center is determined by domain offset parameters. Each domain in an experiment may have an offset. The gamma value in the gamma.def le is adjusted to set the center of the spectrum to the 0 ppm chemical shift reference value with 0 ppm x_offset. To shift the spectral center to 5 ppm, the x_offset is entered as 5 [ppm]. Offsets may be entered in Hz or ppm units. The actual calculation and conversion of the domain and offset parameters is done at run-time in the acquisition system. Spectral (Sweep) Widths The spectral width in a particular domain is determined by domain sweep parameters. In this eld, you may set the observation range (ppm). Each domain in an experiment must have a value. The Eclipse NMR has a dual channel, simultaneous sampling acquisition system. Therefore the x_sweep is given as the total observed spectral width instead of the plus/minus sampling frequency (i.e., 2000 Hz is really +1000Hz). This value can be entered in ppm or Hz. If the value is entered in ppm, it is internally converted into Hz immediately prior to acquisition. Data Points Each domain must also have the number of data points to collect. This is done with the domain points statement. In this eld, you may set the number of data points of the f2 axis. The x_points value must be a power of 2 (for the FFT algorithm). A non-power of two value will automatically be increased to the next higher power of two during collection. The behavior for higher dimensions (y_points, etc.) is determined by the round_points header ag. On the Eclipse, x_points always represents the number of complex pairs, i.e. x_points = 16384 is 16384 complex numbers, each with a real and imaginary part, for a total of 32768 values. For higher dimensions, this value is the number of slices or planes. The collection mode, real or complex, species how the data is collected and may impact the experiment time. Scans The scans parameter determines how many times through the pulse sequence the acquisition will repeat. In the eld, you may set the number of accumulations. For experiments, scans are per slice and not affected by y_points. The maximum number of scans depends on the usage and experiment. Scans may be either positive (inner scans) or negative (outer scans). For one-dimensional experiments there is no difference, except that the maximum limit is different. For multi-dimensional experiments positive (inner) scans means each slice (time increment) is time-averaged for scans times before incrementing to the next slice (conventional 2D acquisition). Negative (outer) scans means after each single acquisition, the counter is incremented to the next slice, and then scans number of passes is made through the entire data set.
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Pulse Section
Table 10-8: Scans Parameter Limits scans positive 0 negative maximum 1073, 791, 824 ... -1,073,741,824 onedimensional 1073, 791, 824 forever 1,073,741,824 two-dimensional inner scans 32768 max 32768 outer scans 32768 max
Prescans Prescans are the number of times through the pulse sequence before the data collection begins. With this eld, you set the number of prescans (dummy scans). The data is discarded after prescans. For one-dimensional data, x_prescans is used. For twodimensional data, both suppressions and y_prescans may be used. x_prescans is executed only on the rst slice and y_prescans is used for the remaining y_points. Normally, y_prescans is not required because there is no delay going from slice to slice in a 2-D experiment, and therefore the equilibrium magnetization does not change. mod_return is a number specifying how often the acquisition data is returned to the workstation and the View tool. If it is 0, then the View Tool never updates. y_points species the number of points in the y dimension of a 2D or 3D experiment. This is often referred to as the number of slices, or t1 increments. No compensation is necessary for hypercomplex (Phase sensitive) 2D experiments. The value of y_points can be altered by the round_points header ag. If round_points = TRUE, then y_points will be rounded to the next higher power of 2 when the experiment is run. x_acq_time y_acq_time x_resolution y_resolution These values are calculated by the std_acquisition include le.The formulae are: x_acq_time = x_points/x_sweep x_resolution = x_sweep/x_points y_acq_time = y_points/y_sweep y_resolution = y_sweep/y_points
PULSE SECTION
The Pulse section of the experiment (Figure 10-9) contains the pulse sequence and virtual
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parameters for the timing of the pulse sequence. Experiments use the concept of virtual parameters. A virtual parameter is usually a time and does not correspond to a hardware parameter, such as a gain or frequency. Virtual parameters exist only within an experiment and are for the convenience of the operator. Virtual parameters may be dened, used, and referenced within an experiment.
Figure 10-9. Experiment Tool Pulse Section total_time The approximate time necessary for measurement is displayed. x_pulse The pulse width actually used for the measurement is displayed. relaxation_delay Set the delay time. j_constant Set the J value. To view the graphical representation of the Pulse sequence: Click on the Pulse button within the pulse section in the experiment tool. This brings up the pulse display widget (Figure 10-10). This widget graphically displays
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Pulse Section
information about the experiment currently loaded into the Experiment Tool. The pulse widget is for display only; it can not be used for entering experiment information, or for making modications to the pulse sequence.
Figure 10-10. Pulse Display Widget The pulse display widget consists of three sections: loop, header, and chart. Solid lines are used to resize individual areas of the chart widget, so that greater or lesser portions of it may be used to display the chart, loop, or header section. Drag the square on the right edge of these bars up or down to change the size of a portion of the widget. In the bottom section, the opening and closing of individual gates within an experiment are displayed. The label to the left of each row of the chart indicates the gate. The labels placed horizontally above the chart show which instruction is being acted on, and how much time this instruction should take. The numbers below these horizontal labels simply indicate the chronological order in which they are carried out. The letter m appears before the number on those instructions which are macros. Instructions containing arrayed values appear with the letter a displayed next to their number. The buttons to the left of the horizontal labels are for acting on the macros, which may be expanded or shrunk individually, or all at once. At the top of the widget are two empty boxes. Clicking on an individual pulse value will
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cause its instruction, any arrayed values, and the time that it will take to appear in the topmost box. Some of the pulses are given multiple angle values; these are outlined. Clicking on an outlined pulse will cause the values of these angles to be displayed in the lower box. Finally, there is a section for displaying the presence of loops within the experiment. If loops are present, they will appear beneath the boxes at the top of the widget. Loops are displayed as solid lines above whichever instructions (including other loops) they enclose. These lines are labelled with as much of the name they were given in the experiment le as will t beneath the line representing them.
SUBMITTING EXPERIMENTS
Verify the settings of the Header, Instrument, Acquisition, and Pulse section elds again. If they are correct, click on the Submit button in the Experiment Tool window to enter the experiment into the Spectrometer Control computers queue. By this operation, measurement starts.
Note: The command for starting an experiment can be issued repeatedly, even if another experiment is currently being collected. After one experiment nishes, the next experiment will be started under the stored experiment conditions. In other words, the spectrometer executes experiments on a rst-in, rst-out basis. Probe Codes and Probe Files Each type of probe has a unique identication code that the spectrometer senses through the Probe Status connector displayed in the Sample tool. This code number is used to look up a probe le specic to a given probe. Each probe le contains unique information about the probe. This information may be accessed and used inside an experiment. The spectrometer probe les are normally found in the /eclipse/probes/ directory on the acquisition system. You must have root privilege on the acquisition computer to edit the probe les. The codes for common probes are listed in Table 10-9.
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Submitting Experiments
Table 10-9: Eclipse Probe Code List Probe Code 1412 1288 1320 1556 1796 2564 Probe Description Standard 5mm TH5 Broadband probe 31P-15N 10mm T10 Broadband 31P-15N 10mm T10L Low frequency 15N-103Rh 5mm 1H 5mm HX5 Inverse 31P-15N Autotune 5mm TH5 Broadband probe 31P-15N
For GX, GSX, and CPF spectrometers retrotted with a Delta Upgrade, the probe codes will be different because only the 8 lower bits are read. The standard GX, GSX and CPF assignments are given below. Note: these are standard CPF values, but they may vary on different spectrometers. Table 10-10: GX, GSX and CPF Assignments Probe Code 53 34 5 69 93 Probe description Standard 5mm TH5 Broadband probe 31P-15N 10mm T10 Broadband 31P-15N 5mm CH Dual probe 5mm 1H 5mm HX5 Inverse 31P-15N
Probe Attributes The rst line in any probe le lists the probe attributes. These attributes are used with the optional probe_attr eld in the Header section. The software also uses this string to check for compatibility between the domains (frequencies) requested and the allowable frequencies on a probe. If the software detects an obvious conict, such as a 13C x_domain on a 1H only probe, the experiment will abort. 90 Degree Pulses
o The default 90 pulses are accessed for viewing only in the Spectrometer Control Tool under Tool-90s:
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90 = 10.0 10.0 50.0 The order of the values is -> observe, high power decoupling (HI), and low power o decoupling (LO). These are the default 90 pulse widths and are used when no matching domain (nucleus) is found in the probe le. If a matching domain is found, then the 90o values inside the domain are used. Spin Lock Pulses The spin_lock_90 and spin_lock_attn parameters are used for setting the parameters for spin lock experiments such as HOHAHA or TOCSY. These spin lock values are always calibrated pairwise, that is for a spin_lock_90 pulse, there is only one spin_lock_attn value. Temperature Limits Each probe may have a different approved variable temperature range. The variable temperature controller may operate over a range larger than that approved for a particular probe. The maximum range of the spectrometer is specied in the machine.config le. The TEMP_LIMIT_HI and TEMP_LIMIT_LO determines the legal range for each probe. The solvent.def le contains the boiling and freezing points for all of the standard deuterated solvents. If the requested temperature exceeds either of these values, a warning message is displayed in the Delta Console and an acknowledge box is displayed. Irr_code The irr_code value determines the maximum decoupler power during three different pulse conditions. The irr_code is a base 10 number derived from the octal (base 8). See Appendix C for details on how to calculate the values. The irr_codes for common probes are: Table 10-11: IRR Codes for Probes Probe Type TH5 T10 T10L H5 HX5 irr_code 146 212 212 128 128
For GX, GSX, and CPF spectrometers retrotted with a Delta Upgrade, only two irr_codes are valid (only the lowest 3 bits are read). Therefore an irr_code
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Submitting Experiments
<= 4 will deliver the 4 watt level, an irr_code >= 5 will deliver the 9 watt level. Domains The domain sections of the probe les are used to store hardware parameters that are specic to the particular nucleus. Any hardware parameters may be entered in the domain sections. The domain sections are denoted by the syntax: domain nucleus .... end domain
o The most common values in the domain section are the 90 pulses. The order is the same as the default 90o pulses - observe, high power decoupling, low power decoupling.
Probe Tuning Values The domain section can also contain the probe tuning values for each nucleus. The tuning values are displayed when the force_tune header ag is true. The values are also used by the autotune probes.
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CALCULATIONS
Calculation of Pulse Widths and Angles Referencing Probe Variables The pulse widths stored in the probe le are referenced in the following way: domain90_modifier where domain corresponds to the x,y,z,a,b,c,d,e and _modifier corresponds to the HI, LO, or no decoupler power. Pulse widths for different nuclei are separated by the domain sections. For example, consider the following statement: x_pulse => x90; This statement means the following: dene a variable x_pulse (normally in keeping with good programming practice, x_pulse would be related to the x_domain, but it could be called something else). assign the value of x90 to x_pulse x90 is a special hardware parameter. It refers to the first value in the set of three numbers after the "90 =" in the probe file in whatever domain section matches the o current x_domain. Each time the domain changes, the new 90 values for that domain are read from the probe file. A second example: x_pulse => x90/2; This is similar to the rst, but the x90 value is part of an expression (divide by 2). A third example: y_pulse => y90_hi; In this case the variable y_pulse (which would normally have something to do with the y dimension of a 2D spectrum) is set to the second value in the set of three 90o pulses for the nucleus specied by the y_domain. A nal example is: irr_pwidth = irr90_lo; In this case, a hardware parameter irr_pwidth is set to the third value in the set of three 90o pulses. In this case the nucleus domain is specied by the irr_domain.
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Calculations
Using Expressions to Calculate Pulse Angles The x90 values may be used as part of other expressions to convert pulse widths into pulse angles. For example: define x_angle => 90`[deg], 1`[deg] -> 720`[deg] :1`[deg] define x_90_width => x90 define x_pulse =? x_90_width * (x_angle / 90`[deg]); In this example, x_angle is assigned to 90 and the legal range is from 1 to 720 in steps of 1 . The displayed value is changeable by the user (=> symbol) in the Experiment Tool. The x_90_width is assigned to the x90 parameter from the probe le and is also changeable by the user. The x_pulse (the actual time duration of the pulse) is calculated from the expression and only displayed (=? symbol) in the Experiment Tool. Calculation of Audio Filter Delays The Eclipse supports two types of hardware audio lters, Butterworth and Bessel. Some of the features of each have been mentioned previously. Following the nal RF pulse but before the rst data point is sampled, several things occur in the spectrometer. First, a time is reserved to let the probe recover from the effect of the RF pulse and to compensate for any pulse breakthrough. This time is called the dead_time and all spectrometer gates are closed. Following the dead_time, a second time period is reserved to open the receiver and stabilize the electronics (i.e. audio lters) before sampling the rst data point. This time is called the delay. Because the spins have begun to precess and evolve starting from the end of the pulse, the values of dead_time and delay can have great impact on the data. Normally, effects are seen in the spectral phasing and in baseline roll.
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The Eclipse uses different formulas for calculating the dead_time and delay depending on the audio lter type. These expressions are in the std_pulse include le. define dead_time = if filter_mode = "BUTTERWORTH" then if 0.6/x_sweep - x_pulse/2 < 15[us] then 15`[us] else 0.6/x_sweep - x_pulse/2 else --BESSEL case 20`[us]; define delay = if filter_mode = BUTTERWORTH then if 0.4/x_sweep < 0.5[us] then 0.5`[us] else 0.4/x_sweep else --BESSEL case 0.6/x_sweep; Total Time Every experiment includes a Total Time calculation. This calculation is performed automatically by the Experiment Tool. The total time is used by the Experiment queue manager for scheduling of the experiment using the rules assigned in the queue.hours le. If the time calculation seems in error, check the collect statement and the number of buffers for the experiment.
PHASE TABLES
The RF signals from an NMR spectrometer may have frequency, phase, and amplitude characteristics. The frequency is controlled by the domain and offset. The phases are controlled by variables in the experiment. Once a phase variable is dened it may be used multiple times in a single experiment. Phases are dened as sets using the brace {} syntax. Refer to the section on multiple buffers for information on nested braces. For example: define phase_1 = {0, 90, 180, 270}; Parentheses provide a shorthand notation for repeated phases: define phase_2 = {4(0),4(180)};
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Phase Tables
This expands to: define phase_2 = {0,0,0,0,180,180,180,180}; Parentheses may also be nested: define phase_3 = {2(2(0), 4(180), 2(0)), 2(2(90),4(270),2(90))}; This expands to: define phase_3 = {2(0,0,180,180,180,180,0,0), 2(90,90,270,270,270,270,90,90)}; Which, upon further expansion, becomes: define phase_3 = {0,0,180,180,180,180,0,0, 0,0,180,180,180,180,0,0, 90,90,270,270,270,270,90,90, 90,90,270,270,270,270,90,90}; The maximum phase table length is 255 steps. Concatenation of Phase Sets Using the concatenation operator ||, multiple sets of phases may be concatenated together. For example: define a = {0, 90, 180, 270}; define b = {270, 180, 90, 0}; define phase_1 = a||b; --The result of the define phase_1 is: --phase_1 = {0,90, 180, 270, 270, 180, 90,0} Addition of Phase Sets A constant value may be added to any phase. The addition is distributed across the entire set of phases. For example: define a = {0, 90, 180, 270}; define phase_1 = a+90; --The result of the define phase_1 is: --phase_1 = {90, 180, 270, 0}
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90 Degree Phases Most phase tables are constructed with quadrature (90o) steps. For example: define phase_1 = {0,90,180,270}; Sub-90 Degree Phases The Eclipse spectrometer can be equipped with sub-90o phase shifters. These are normally o o o 30 , 45 , 60 within each quadrant. Therefore, phases of 0, 30, 45, 60, 90, 120,135, 150, 180, 210, 225, 240, 270, 300, 315, and 330o can be generated. The phase sets are created in the normal way: define phase_4 = {0,45,90, 135, 180, 225, 270, 315}; Note: The sub-90o phases use additional hardware lines in the pulser. This o assignment is done automatically by the experiment compiler. When sub-90 phases are used it is possible to exhaust assignable pulser lines such that the experiment will not execute.
MULTIPLE BUFFER ACQUISITION

In many experiments, multiple data collections are required while changing a single variable such as a phase and keeping the data in separate locations. Data collected in this way are said to be multiple buffer acquisitions. The number of buffers is determined by the nested braces around a variable. For example, a two-buffer phase experiment could be written as follows: define phase_6 = {{0, 180}, {90, 270}}; The pulse sequence will cycle through all buffers on each scan, then increment the scan counter. Thus the total number of acquisitions is equal to scans * buffers. Incrementation of phases is done on scans, not buffers. Multiple buffer acquisitions also use the collection mode for data routing in multidimensional experiments. For example: define phase_1 = {{ 0, 180, 180, 0},{90, 270, 270, 90}}; define phase_2 = {2(0), 2(180)}; define phase_acq ={0, 180, 180, 0};
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module_config Options
Table 10-12: Multiple Buffer Phase Cycles buffer 1

scan phase_1 phase_2 phase_acq phase_1
buffer 2
phase_2 phase_acq
1 2 3 4
0 180 180 0
0 0 180 180
0 180 180 0
90 270 270 90
0 0 180 180
0 180 180 0
MODULE_CONFIG
OPTIONS
Each module in the Eclipse spectrometer has options that can be set to achieve different features. These options are controlled by the module_config parameter. Because the options are often channel specic, they are labeled with the output channel. Hardware Options The module_config options are composed of a prefix.feature. The prex is the RF channel (OBS, IRR, TRI) for the particular feature. Multiple features may be applied by adding additional strings. The order is not important. However, if any feature is set, all desired features, including .normal, must be set. Table 10-13: RF Channel settings Mode CHECK NORMAL CW ATN FINE_PHASE1 FINE_PHASE2 SPIN_ECHO SOLID_SHAPER SOLID_SAMPLE Function Check mode, normally not used. Must be set if any non-check feature is set. CW mode - RF on continuously. Attenuator on. RF ne phase shift offset 1. RF ne phase shift offset 2. Used in solids experiments. Used in solids experiment, OBS only. Species there is a solids probe connected. The machine will enforce a match probe type (solids/ liquids) and an export type (solids/liquids).
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Table 10-14: Time-shared Homonuclear Decoupling Mode TIME_SHARE CYCLE_10KHZ CYCLE_TIME_SYNC Function Activates RF time sharing. Cycles between the offset frequencies at 10kHz digital. Cycle between the offset frequencies synchronized with the time-share pulse digital offset unit only.
Table 10-15: Noise Modulation Gating Mode IRR and TRI channels only NOISE1 NOISE2 RF noise source offset 1 - noise modulation only. RF noise source offset 2 - mod controlled by rf_mod. Table 10-16: Amplier Power Settings Mode AMP_NORMAL AMP_LOW_PWR OBS amp Only ROUTE_IRR ROUTE_TRI IRR & TRI amp only AMP_9W AMP_HOMO AMP_BILEVEL AMP_FULL_PWR AMP_INEPTCHK Enables 9watt mode (vs. 4watt default). Enables homonuclear decoupler power mode. Turns on bi-level power switching mode. Enables full power mode. Enables inept check mode. Table 10-17: Combination Features Mode CW_NOISE Function Combinations NORMAL, CW, and NOISE1 Route check mode from IRR through OBS. Route check mode from TRI through OBS. Function AMP normal power mode. Low power mode for amps. Function
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Collection Mode
Table 10-17: Combination Features Mode HIGH_PWR Function Combinations NORMAL, NOISE2, and AMP_FULL_PWR
COLLECTION MODE
The COLLECT statement is used to ensure that the data is collected properly in each dimension and referenced properly to the RF channel for the dimension. The order is implied to be (x y z a b c d e). Each dimension is separated by a space, and the values within each domain are separated by commas. For example, a typical one-dimensional experiment can be written as: collect complex, obs; The Eclipse always collects the x domain as complex vectors and normally the observe channel OBS generates the x_domain RF. For a typical two-dimensional absolute value experiment: collect complex, obs real, obs; -- cosy or collect complex, obs real, irr; -- ch-correlation For a phase sensitive two-dimensional experiment: collect complex, obs complex, obs; By default the Eclipse presents all multidimensional data in a p-type format; i.e., the 0 ppm (high eld) coordinate in the upper right corner and the axis units increasing to the lower left corner as the operator views the data. If a phase cycle results in a reversed presentation, use the NTYPE collection mode to reverse the sense of the axis. collect complex, obs real, irr, ntype; One could alternatively use the REVERSE Percival command during data processing to correct the presentation.
MACROS
As discussed in an earlier section, the pulse sequences may reference macro programs, either from inside the experiment or via include les. A macro used in almost all experiments is the acq macro: macro acq ( dead_time, delay, phase ) is dead_time, (reset); delay, (reset,rcv.gate); acquire (reset,rcv.phs.phase); end acq;
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PULSE PROGRAMS
Specications The Eclipse with the PGX-300 pulser has the following specications: Table 10-18: PGX-300 Pulser Specications Pulse Control time state range time state setability time state precision loop precision jump precision output gates loop range Specication 0.3 us to 429 sec 0.1 us 0.2 us 0.3 us 0.2 us 20 0 to 4095
Begin/end Statement The pulse sequence is marked with a begin statement. The pulse sequence terminates with an end pulse; statement. Time States The Eclipse pulse sequences are series of variables representing time delays followed by a list of gate assignments which describe the desired RF behavior during the particular time delay. The delays are called time states. Each line after the begin statement represents either a time state, output gates, or both. Referencing Time Variables A variable is assigned to a time state by simply using the name: begin initial_wait; ... end pulse In this example, the time value previously assigned to initial_wait is executed. Referencing Spectrometer Parameters A hardware time parameter, such as x90, may be used directly: begin x90; ... end pulse
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Gate Assignments and Options
In-line Calculations Calculations may be performed in the pulse sequence. The calculations are evaluated when the experiment is compiled just prior to execution. begin ... 1/(2*j_constant); ... end pulse In this example, the time delay will be the reciprocal of twice the j_constant variable (Hz). Note that the parentheses are required to order the mathematical operations properly. End of Sequence At the end of the pulse sequence, all gate lines are closed before the jump back to the beginning of the sequence.
GATE ASSIGNMENTS AND OPTIONS

The gate assignments controlled by the pulser are directly wired to various hardware features. Each time state may be followed with the gate conditions during that time state. The gates remain open only for the duration of the time state. To set a gate on or off for multiple time states, use the ON or OFF statement. The ON or OFF statement can be used to set conditions without a time state. The Eclipse has a total of 20 output gates. Many of the output lines have xed assignments; others are automatically assigned by the Experiment compiler. The general syntax for gate conditions is: time_state, (channel.feature.variable); Note: the comma after the time state is required. If the comma is missing, a syntax error will occur and experiments will not compile. Multiple gates on a single time state are specied by listing them inside the parentheses: time_state, (channel.feature.variable, channel.feature.variable,...); The on and off statement syntax is: on (channel.feature.variable); off (channel.feature.variable); Multiple gates may be listed inside the on and off statements.
Note: There is no comma after the ON or OFF.
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RF Gates The RF gates are called by using channel.gate. For example: obs.gate irr.gate tri.gate RF Phase The RF phases are called by the channel.phs.variable, where channel is one of the RF channels and variable is the name of a phase list. For example: obs.phs.variable irr.phs.variable tri.phs.variable Attenuators Each of the RF channels has a variable attenuator. The attenuator values range from 0[dB] (no attenuation) to 64[dB] (maximum attenuation, minimum power) in 0.125 dB steps. The attenuator value must be dened as a virtual parameter. For example: obs.atn.variable irr.atn.variable tri.atn variable Note: The Experiment compiler automatically detects the use of an attenuator and sets the module_config parameters accordingly. Frequency Offset The RF may be switched between two frequency locations using chan.offset.variable. The channels are limited to the decoupler channels. For example: irr.offset.variable tri.offset.variable
the
Noise Modulation Each of the decoupling channels can be modulated to provide broadband decoupling. The modulation parameters are listed as hardware parameters and the modulation sequence are programmed in ROM.
10-46
Gate Assignments and Options
Table 10-19: Irradiation Modulation Modes Mode IRR_PWIDTH IRR_NOISE TRI_PWIDTH TRI_NOISE Description
o 90 pulse width at the IRR decoupler power level
IRR noise modulation - Waugh, Waltz, Square wave 90o pulse width at the TRI decoupler power level TRI noise modulation - Waugh, Waltz, Square wave
The noise modulation is controlled separately from the RF gate. The default condition of all experiments is noise modulation off. To activate continuous noise modulation use the module_config variable chan.noise1. For example: module_config = irr.normal, irr.noise1; This method sets the modulation on continuously, but the RF gate is controlled independently. Other experiments require the pulse sequence to switch from CW to noise modulation during the sequence. This is done using a combination of the module_config and rf_mod gate line: module_config = irr.normal, irr.noise2; ... on (irr.rf_mod); -- activate noise off (irr.rf_mod); -- deactivate noise Acquisition Macro The acquisition macro controls specic gate lines - reset, rcv.gate, rcv.phs. The reset line initializes the counters and phase tables for acquisition, the rcv.gate line opens the receiver, and the rcv.phs.variable controls the receiver phase. macro acq ( dead_time, delay, phase ) is dead_time, (reset); delay, (reset,rcv.gate); acquire (reset,rcv.phs.phase); end acq; Interactions with irr_code and module_cong If the AMP_FULL_PWR mode is invoked in any of the module_config options, the pulse power level is determined by the rst value of the irr_code parameter. In order to
10-47
protect the probe from excessive power (damage from arcing), a special hardware gate is used in high power sequences during the Decapolis period. The rf_limit gate is used to drop the decoupler power from the high power level to the acquisition level for decoupling (third value in irr_code). For example: on (irr.rf_limit); ... off (irr.rf.limit); On GX, GSX, and CPF spectrometers (Delta Upgrade) the rf.limit bit does not work the same way on the irr channel. Therefore, if amp_full_pwr is used in any way, an attenuator must also be used to reduce the decoupling power. On any Delta Upgrade spectrometer (GX, GSX, CPF) exercise extreme caution until the decoupler power levels are independently measured with a power meter or an oscilloscope. Refer to Appendix D for more information.
COMPILING AND ERROR MESSAGES

When the experiment is loaded into the Experiment tool, the text is interpreted and the user-changeable variables are displayed. If the Experiment detects an error in the le, an error message will be placed in the screen and information about the error will be displayed in the Delta console window. When the experiment is submitted to the spectrometer, it is held in the experiment queue. When the experiment comes to the top of the queue for execution, it is compiled into a form the pulser understands and then executes.
ARRAYED PARAMETERS
Often an operator wants to vary one or more parameters while repeating the same experiment. The Eclipse allows the operator to input an array of values into a single parameter in the Experiment Tool. An arrayed parameter allows you to collect multiple data sets while systematically varying one or more experiment parameters. The data from an arrayed parameter experiment may be stored as multiple les or as a single multi-dimensional le. The entire experiment is repeated for each value in the array. When the experiment is run, the acquisition system will detect the arrayed parameter as a virtual dimension. Interaction with multi_le Option If the multi_file option in the header is true in an experiment, each separate dataset from an arrayed parameter experiment is returned as a separate le. If the multi_file
10-48
Arrayed Parameters
option is false, the arrayed parameter data set is returned as a single multi-dimensional le with virtual dimensions. The normal Delta processing tools may be used with the virtual dimension data sets, except for processing in a non-linear dimension. Syntax An arrayed parameter may be created with most experiment variables by the array command. The command is of the form y_acq, where y denotes that the array will become the y_domain of a pseudo-2D data set. Likewise an arrayed parameter for a two-dimensional experiment is denoted by z_acq, thus creating the z_domain of a pseudo-3D data set. Likewise, there are a_acq, b_acq c_acq, d_acq, and e_acq. The array statements can be nested, the outermost array is performed before each increment of the inner arrays. Following the array statement is the set of the arrayed values in brackets. The list can be either discrete values, or a range with a step size, for example: y_acq {5, 10, 15, 20}. The Experiment Tool will check to see if an arrayed list can be expressed as a range. If it can, then a range is displayed: y_acq {5 -> 20 : 5} Arrayed parameters are entered either directly in the Experiment Tool eld, or in a popup window obtained by clicking on the parameter name. For example: Clicking on the scans parameter produces a window like the one on page 10-51, from which the user may enter the array either as a set: {value1, value2, value3,...} or as a range with a {start value -> stop value: step size} When using parameters with units, at least one of the values must have a unit. If only one unit is specied, the Experiment Tool applies that unit to all values. If different units are desired, all values must have units specied.
10-49
After the array is entered, the parameter entry in the Experiment Tool will change to:
if the entered data can be ranged, or
if the entered data cannot be ranged. To modify an existing array, place the cursor in the window, or click on the parameter name. If the array is too long to t in the window, it scrolls off the edge. Use the Home and End keys to move from one end to the other.
EXCEPTIONS TO ARRAYED PARAMETERS

The only values that cannot be arrayed are parameters that affect the size or data point sampling of the le. This includes domains, sweep widths, and points.
SETTING ARRAY PARAMETERS

The Set Array Parameters Window (Figure 10-11) comes up when you select a parameter that can be arrayed (otherwise, a simple box with the value which cannot be arrayed will come up). Parameters can be arrayed for an experiment of up to eight dimensions. Use the Pick cursor mode to cut and paste values into the Set Array Parameters Window from an open geometry with data. To remove a value from the value list, select the value and press the Remove button. Selecting Clear will remove all values from the
10-50
Collecting T1 Data
list. Use the Set Value button to update the arrayed parameters in the experiment. Cancel to cancel this setting. All available dimensions are displayed in the dimension box to the left of the window; the top dimension is the default setting. Array Types can be represented in Linear, Exponential or Logarithmic form, with Start and Stop values, and a Step increment. To bring up this screen, toggle off the Listed Box.
Figure 10-11. Set Array Parameters Windows
COLLECTING T1 DATA
Because the data set can only be collected in the x-y plane, we have to set up an array of tau values for the experiment to collect T1 data. To collect data for T1_analyze: Use either
/usr/people/jeol/nm8901/global/experiments/1d_more_exp/double_pulse.exp
or
/usr/people/jeol/nm8901/global/experiments/1d_more_exp/ double_pulse_dec.exp
Note: double_pulse_dec.exp is used for carbon atoms.
1. First, try using the arrayed parameter pop-up box (click on the tau_interval button to bring up the pop up box.) 2. Or, enter the arrayed tau_interval parameter manually. The parameter is arrayed in the following fashions: y_acq{0.1->20:0.5[s]}, i.e., 01[s] -> 20[s] in 0.5[s] steps. or y_acq{0.1[s], 0.2[s], 0.3[s]....} which sets the tau value explicitly. This arrayed parameter can be entered using the arrayed parameter pop up box (click on the tau_interval button to bring up the pop up box.)
10-51
3. Last, set up the rest of the parameters of the experiment as usual. After the pseudo 2D data set is uploaded, use 1D slice to process the rst slice and phase in the x_domain. Subsequently, the processing list along with the phase information is applied to the remaining slices by sending the processed data to the data slate. Then the data can be ported into T1 Analyzer for relaxation analysis.
10-52
APPENDIX A: STANDARD INCLUDE FILES

The following les can be found in the directory.
STD_ACQUISITION
/usr/delta/global/experiments/
/usr/delta/global/experiments/std_acquisition
---------------------------------------------------------------------------------Experiment Source Code --Delta NMR Experiment & Machine Control Interface ----Copyright (c) 1996 JEOL USA, Inc. --All Rights Reserved ----------------------------------------------------------------------------------
-- std_acquisition --- Standard Experiment Acquisition include file -filter_width = x_sweep/2; x_acq_time =? x_points/x_sweep; x_resolution =? 1/x_acq_time;
STD_2D_ACQUISITION
/usr/delta/global/experiments/std_2d_acquisition
-- std_2d_acquisition --- Standard Experiment 2D Acquisition include file -y_acq_time =? y_points/y_sweep; y_resolution =? 1/y_acq_time;
A-1
STD_3D_ACQUISITION
/usr/delta/global/experiments/std_3d_acquistion
-- std_3d_acquisition --- Standard Experiment 2D Acquisition include file -z_acq_time =? z_points/z_sweep; z_resolution =? 1/z_acq_time;
SET_DEC_INSTRUMENT
/usr/delta/global/experiments/std_dec_instrument
-- std_instrument --- Standard Experiment Instrument include file -solvent => #; filter_mode = BUTTERWORTH; recvr_gain => 15; irr_noise => WALTZ; tri_noise = WALTZ;
A-2
std_domains
STD_DOMAINS
/usr/delta/global/experiments/std_domains
-- std_domains -- domain Proton Deuterium Lithium7 Boron11 Carbon13 Nitrogen15 Oxygen17 Fluorine19 Aluminum27 Silicon29 Phosphorus31 Rhodium103 Cadmium113 Tin119 Xenon129 Tungsten183 Platinum195 Mercury199 Lead207
offset 5[ppm] 5[ppm] 0[ppm] 0[ppm] 100[ppm] 0[ppm] 0[ppm] 0[ppm] 0[ppm] 0[ppm] 0[ppm] 0[ppm] 0[ppm] 0[ppm] 0[ppm] 0[ppm] 0[ppm] 0[ppm] 0[ppm]
sweep 15[ppm] 15[ppm] 20[ppm] 250[ppm] 250[ppm] 600[ppm] 600[ppm] 400[ppm] 500[ppm] 500[ppm] 700[ppm] 1000[ppm] 800[ppm] 1000[ppm] 1000[ppm] 1000[ppm] 1000[ppm] 1000[ppm] 1000[ppm]
STD_DOMAIND_MASTER_LIST
/usr/delta/global/experiments/std_domains_master_list
This file is used only for reference when updating the std_domains file.
A-3
STD_HEADER
/usr/delta/global/experiments/std_header
-- std_header --- Standard Experiment Header include file ---allow_copy = true; auto_dwell = true; --auto_filter = false; auto_gain => false; --automatic = false; --create_file = true; --comment = ; --destination = ; --eject = false; --filename = ; --filter_limit = 0; --filter_start = 0.0; --filter_stop = 0.0; --filter_wide = false; force_tune => false; --force_vector = false; --hold = false; --init_group = 0; --job_group = false; --load_pulser = true; --load_shims = false; --lock_check = false; --match = true; --module_config = ; --multi_file = false; --not_owned = false; --pre_post = true; --probe_attr = ; --process = ; --process_copy = true; --quick_tune = false; --repeat = false; --resubmit = false; --round_points = true;
A-4
std_instrument
--sample_id save_aborted --sawtooth --settle_vt --slot --sn_border --sn_noise_start --sn_noise_stop --sn_ratio --sn_signal_start --sn_signal_stop --sn_skip --start_time vector
= = = = = = = = = = = = = =
; true; false; false; 0; 100; 0.0; 0.0; 0; 0.0; 0.0; 10; ; true;
STD_INSTRUMENT
/usr/delta/global/experiments/std_instrument
-- std_instrument --- Standard Experiment Instrument include file -solvent => #; filter_mode => BUTTERWORTH; recvr_gain => 15; irr_noise = WALTZ; tri_noise = WALTZ;
STD_PULSE
/usr/delta/global/experiments/std_pulse
-- std_pulse --- Standard Experiment Pulse include file -macro acq ( dead_time, delay, phase ) is
A-5
dead_time, (reset); delay, (reset,rcv.gate); acquire (reset,rcv.phs.phase); end acq; define dead_time = if not auto_dwell then if filter_mode = BUTTERWORTH then if 0.6/x_sweep - x_pulse/2 < 15`[us] then 15`[us] else 0.6/x_sweep - x_pulse/2 else 20`[us] else 0`[us]; = if not auto_dwell then if filter_mode = BUTTERWORTH then if 0.4/x_sweep < 0.5`[us] then 0.5`[us] else 0.4/x_sweep else 0.6/x_sweep else 0`[us];
define delay
define phase_preset = 2`[us];
STD_SOLID_INSTRUMENT
-- std_instrument --- Standard Experiment Instrument include file --- solvent => #; filter_mode = BUTTERWORTH; recvr_gain => 15; irr_noise = WALTZ; tri_noise = WALTZ;
A-6
APPENDIX B: INSTRUMENT PARAMETERS

This table lists the spectrometer machine parameters. For specific information regarding these parameters, please contact JEOL applications. FILTER_MODE FILTER_WIDTH HE_LEVEL HF_MATCH_DIAL HF_TUNE_DIAL IRR90 IRR90_HI IRR90_LO IRR_CODE IRR_NOISE IRR_PWIDTH ITERATIONS LF_MATCH_DIAL LF_TUNE_DIAL LOCAL_TIME LOCK_ACHIEVE_POINT LOCK_GAIN LOCK_LEVEL LOCK_OSC_OFFSET LOCK_OSC_STATE LOCK_PHASE LOCK_SETTLE_POINT LOCK_STATE LOCK_STATUS LOCK_STRENGTH N2_LEVEL NUM_SCANS OBS_NOISE OBS_PWIDTH ORDERS PASS_RIPPLE PROBE_ATN PROBE_COARSE PROBE_ID PROBE_MATCH PROBE_TUNE QUA90 QUA90_HI QUA90_LO QUA_NOISE QUA_PWIDTH RECVR_GAIN SAMPLE_ACTION
A90 A90_HI A90_LO ADC_CARD AUTOLOCK_LEVEL AUTOSHIM_DELAY AUTOSHIM_MODE AUTOSHIM_TRACK AUTOTUNE_DIAL_STATE B90 B90_HI B90_LO BBUS_INTERFACE_IN_0 BBUS_INTERFACE_IN_1 BBUS_INTERFACE_IN_2 BBUS_INTERFACE_IN_3 BBUS_INTERFACE_OUT_0 BBUS_INTERFACE_OUT_1 BBUS_INTERFACE_OUT_2 BBUS_INTERFACE_OUT_3 C90 C90_HI C90_LO CHANGER_SAMPLE CHANGER_SAMPLE_UNLOAD D90 D90_HI D90_LO DEUT_GRAD_SHIM_90 DEUT_GRAD_SHIM_ATTN E90 E90_HI E90_LO END_TIME EXPERIMENT FACTORS FIELD_STRENGTH
DELTA Users Guide, v3.2 B-1
SAMPLE_STATE SAMPLE_STATUS SAWTOOTH_RANGE SHIM_MAX_RECALL SHIM_NAMES SHIM_X SHIM_X2 SHIM_X2Z SHIM_X2Z2 SHIM_X2Z3 SHIM_X2Z4 SHIM_X3 SHIM_X3Z SHIM_X3Z2 SHIM_X3Z3 SHIM_X4 SHIM_X4Z SHIM_X4Z2 SHIM_XZ SHIM_XZ2 SHIM_XZ3 SHIM_XZ4 SHIM_XZ5 SHIM_Y SHIM_Y2 SHIM_Y2Z SHIM_Y2Z2 SHIM_Y2Z3 SHIM_Y2Z4 SHIM_Y3 SHIM_Y3Z SHIM_Y3Z2 SHIM_Y3Z3 SHIM_Y4 SHIM_Y4Z SHIM_Y4Z2 SHIM_YZ SHIM_YZ2 SHIM_YZ3 SHIM_YZ4 SHIM_YZ5 SHIM_Z0 SHIM_Z1 SHIM_Z2 SHIM_Z3 SHIM_Z4
SHIM_Z5 SHIM_Z6 SHIM_Z7 SHIM_Z8 SOLVENT SPIN_ACTION SPIN_GAS_SOURCE SPIN_GET SPIN_LOCK_90 SPIN_LOCK_ATTN SPIN_SET SPIN_STATE SPIN_STATUS STOP_RIPPLE TEMP_ACTION TEMP_AMBIENT TEMP_BOILING TEMP_COMP TEMP_DELAY TEMP_GET TEMP_LIMIT_HI TEMP_LIMIT_HI_MAX TEMP_LIMIT_HI_MIN TEMP_LIMIT_LO TEMP_LIMIT_LO_MIN TEMP_LIMIT_MD_MAX TEMP_LIMIT_MD_MIN TEMP_MELTING TEMP_RAMP_STEP TEMP_RAMP_WAIT TEMP_SET TEMP_STATE TEMP_STATUS TRANSITION_RATIO TRI90 TRI90_HI TRI90_LO TRI_NOISE TRI_PWIDTH VT_PID_LONG_0_H_CBH VT_PID_LONG_0_H_CBL VT_PID_LONG_0_H_HC VT_PID_LONG_0_H_HL VT_PID_LONG_0_H_PB VT_PID_LONG_0_H_TD VT_PID_LONG_0_H_TI
B-2 Delta Users Guide, v3.2
VT_PID_LONG_0_M_CBH VT_PID_LONG_0_M_CBL VT_PID_LONG_0_M_HC VT_PID_LONG_0_M_HL VT_PID_LONG_0_M_PB VT_PID_LONG_0_M_TD VT_PID_LONG_0_M_TI VT_PID_LONG_40_H_CBH VT_PID_LONG_40_H_CBL VT_PID_LONG_40_H_HC VT_PID_LONG_40_H_HL VT_PID_LONG_40_H_PB VT_PID_LONG_40_H_TD VT_PID_LONG_40_H_TI VT_PID_LONG_40_M_CBH VT_PID_LONG_40_M_CBL VT_PID_LONG_40_M_HC VT_PID_LONG_40_M_HL VT_PID_LONG_40_M_PB VT_PID_LONG_40_M_TD VT_PID_LONG_40_M_TI VT_PID_STD_NB_H_CBH VT_PID_STD_NB_H_CBL VT_PID_STD_NB_H_HC VT_PID_STD_NB_H_HL VT_PID_STD_NB_H_PB VT_PID_STD_NB_H_TD VT_PID_STD_NB_H_TI VT_PID_STD_NB_L_CBH VT_PID_STD_NB_L_CBL VT_PID_STD_NB_L_HC VT_PID_STD_NB_L_HL VT_PID_STD_NB_L_PB VT_PID_STD_NB_L_TD VT_PID_STD_NB_L_TI VT_PID_STD_NB_M_CBH VT_PID_STD_NB_M_CBL VT_PID_STD_NB_M_HC VT_PID_STD_NB_M_HL VT_PID_STD_NB_M_PB VT_PID_STD_NB_M_TD VT_PID_STD_NB_M_TI VT_PID_STD_WB_H_CBH VT_PID_STD_WB_H_CBL VT_PID_STD_WB_H_HC VT_PID_STD_WB_H_HL
VT_PID_STD_WB_H_PB VT_PID_STD_WB_H_TD VT_PID_STD_WB_H_TI VT_PID_STD_WB_L_CBH VT_PID_STD_WB_L_CBL VT_PID_STD_WB_L_HC VT_PID_STD_WB_L_HL VT_PID_STD_WB_L_PB VT_PID_STD_WB_L_TD VT_PID_STD_WB_L_TI VT_PID_STD_WB_M_CBH VT_PID_STD_WB_M_CBL VT_PID_STD_WB_M_HC VT_PID_STD_WB_M_HL VT_PID_STD_WB_M_PB VT_PID_STD_WB_M_TD VT_PID_STD_WB_M_TI X90 X90_HI X90_LO Y90 Y90_HI Y90_LO Z90 Z90_HI Z90_LO
Delta Users Guide, v3.2 B-3
B-4 Delta Users Guide, v3.2
APPENDIX C: IRRADIATION CODES

The irr_codes are the base 10 representation of the octal number determined by the table below. Table 10-1: Irradiation Codes high power decoupler level bits 7 0 0 1 1 6 0 1 0 1 2watt 4 watt 9 watt full power non-acquisition level 5 0 0 0 0 1 1 4 0 0 1 1 0 0 3 0 1 0 1 0 1 0.5 watt 1.0 watt 1.5 watt 2.0 watt 4.0 watt 9.0 watt acquisition level 3 0 0 0 0 1 1 2 0 0 1 1 0 0 1 0 1 0 1 0 1 0.5 watt 1.0 watt 1.5 watt 2.0 watt 4.0 watt 9.0 watt
This chart gives the octal number, not the actual Eclipse irr_code. For example, the TH5 probe requires a 9 watt high power pulse and 1.5 watts of decoupling for both nonacquisition and acquisition times. Therefore the bit settings are as follows: Table 10-2: Conversion Example for TH5 Probe bits binary octal 7 6 1 0 2 5 4 3 0 1 0 2 2 1 0 0 1 0 2
To convert the octal value to decimal (base 10): 2228 = 2*(64) + 2*(8) + 2*(1) = 14610 Thus the correct irr_code for the TH5 probe is 146. The high power decoupler pulses are active only when the correct feature is activated in the module_config line. For GX, GSX, and CPF spectrometers retrotted with a Delta Upgrade, only two irr_codes are valid (only the lowest 3 bits are read). Therefore, an irr_code <= 4 will deliver the 4 watt level and an irr_code >= 5 will deliver the 9 watt level.
C-1
C-2
APPENDIX D: DECOUPLING ON A GX, GSX, OR CPF DELTA UPGRADE SPECTROMETER

The amplier control unit in the GX, GSX, and CPF spectrometers is much more limited than the EX (Eclipse) spectrometer. For all GX, GSX, and CPF Delta upgrades, verify the GSX_COMPAT ag in the machine.config le is set TRUE and the comment characters (--) are removed. This information is provided for reference use only. Because of the wide variety of ages of GX, GSX, and CPF instruments, and thus a variety of PROMs in the amplier control unit, any information given here must be veried with an RF power meter or oscilloscope before the Delta Upgrade is completed. Not all GX and GSX spectrometers are equipped to do all the experiments listed herein. The user is urged to read and understand all of the material before making modications to any experiments. If a user has any doubts about making changes to an experiment, please contact either the JEOL NMR Applications department or the JEOL NMR Service department prior to making the modications.
PROTON DECOUPLING FROM EITHER IRR OR TRR CHANNEL

The GX amplier control unit supports only two power levels, a nominal 4 watt and a nominal 9 watt level. This is true for both decoupler channels with running 1H. The irr_code control for these levels is: Table D-1: GX Decoupler Amplier Control irr_code less than or equal to 4 greater than or equal to 5 power level 4 watt level 9 watt level att&sum adjustment VR6 VR7
If the system is to be used with current generation probes, we recommend reducing the 4 watt level to approximately 2 watts. With Waugh or Waltz decoupling, 2 watts will provide more than sufcient bandwidth for normal use. If the system will be used with older style probes, 4 watts may be necessary, however it is always best to reduce the amount of power.
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HIGH POWER 1H DECOUPLER SEQUENCES FROM EITHER IRR OR TRR

CHANNEL
High power decoupler sequences are those that used an IRAPC value of 100 or greater in the PEGS pulse program. In that mode the ampliers delivered a full RF power to the probe. This mode corresponds to the amp_full_pwr in the Delta pulse language. On GX and GSX spectrometers, no facility exists for automatically reducing the decoupler power during the acquisition. Thus, a separate attenuator line must be used to reduce the RF power during the acquisition if broadband 1H decoupling is used. Do not run a high power sequence until the power levels and attenuator are measured with a power meter. Failure to observe this important difference will result in damage to your probe. If you plan to use high power decoupler sequences, take special precaution to determine the power levels in a dummy RF load rst. The user is urged to read and understand all of the material before making modications to any experiments. If a user has any doubts about making changes to an experiment, please contact either the JEOL NMR Applications department or the JEOL NMR Service department prior to making the modications.
BILEVEL 1H DECOUPLING
Bilevel control is done on both the GSX and EX systems with the PEGS bit 7. Bit 7 is called rf_limit in the Eclipse experiments. When the machine_config bilevel option is enabled, and the rf_limit gate is ON, the 1H decoupler RF level is set to ACQTM level on EX and 9 watt level on GSX. When the rf_limit is OFF, the decoupler power is NON-ACQ on the EX and 4 watt on the GSX. On a GX, GSX or CPF, if the irr_code = 4 (4 watt level), then the bilevel bit will have no effect, if the irr_code = 7 (9 watt level) for a probe, then the bilevel bit will allow the rf_limit bit to become active. On the GX, GSX or CPF spectrometers, to get bilevel control below the 4 watt level, the normal oscillator attenuators must be used and a special GSX experiment is required.
LOW FREQUENCY (X-NUCLEUS) DECOUPLING FROM THE TRR CHANNEL

This section describes certain features and options of the spectrometer that, when used incorrectly, could damage certain NMR probes. The user is urged to read and understand all of the material before making modications to any experiments. If a user has any doubts about making changes to an experiment, please contact either the JEOL NMR Applications department or the JEOL
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Low frequency (X-nucleus) decoupling from the TRR channel
NMR Service department prior to making the modications. This section is applicable ONLY to GX, GSX or CPF systems that are modied to do reverse detection or X-nucleus decoupling experiments. If you are not sure about your system, contact the JEOL NMR Service department. If the spectrometer is modied and equipped to do reverse detection, the power levels from the TRR (X channel) must be veried. The IRR channel is capable of running only 1H, however the TRR channel can accept any oscillator. A major difference exists with the LF channel. Depending on the PROM, rf_limit may work on the TRR channel when generating LF frequencies. This must be veried on each instrument that does X-nucleus decoupling. Set the LF decoupler power with the rf_limit level with VR2 on the att&sum unit.
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APPENDIX E: DIRECTORIES AND FILES USED BY DELTA

This appendix describes the directories and les used by the Delta NMR processing software and the Eclipse NMR spectrometer. The major divisions are the user account, the system Delta directories, and the Eclipse spectrometer directories.
DELTA USER ACCOUNT

Delta is the normal login account for users. ./delta/ This the top directory for user-specic les. These directories are created by the default copy_setup script le and are used as the initial default locations for le requests by the user or a Delta program. ./delta/library/ This is the default user directory which contains the users function library. It contains the compiled Percival programs, the local Percival operators (.l files), and the local_percival_operator_library.1 file. This directory is declared by the LIBRARY flag in the .delta_configure file. ./delta/p_les/ This is the default user directory which contains the source for user Percival programs and operators. This directory is declared by the SOURCE flag in the .delta_configure file. ./delta/process_lists/ This is the default user directory which contains the processing lists for the process_oned and process_nd tools and the process_local_list operator. This directory is declared by the PROCESS_LIST flag in the .delta_configure file. ./delta/templates/ This is the default user directory which contains user-defined templates for tools that need them (2DViewer, 3DViewer, etc.) -- plotter layout templates for the plot tool and user templates for data_slate displays. This directory is declared by the TEMPLATE flag in the .delta_configure file. ./delta/experiments/ This is the default user directory which contains the local user-written experiments for the Eclipse NMR Spectrometer. This directory is declared by the EXPERIMENT flag in the .delta_configure file. ./delta/instrument/ This is the default user directory which contains the user Shim files and other related user instrument files. This directory is declared by the INSTRUMENT flag in the .delta_configure file.
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./delta/reports/ This is the default user directory which contains the user-produced reports generated by Delta, including plots to files, output from the peak spreadsheet database, or reports from Percival programs or functions. This directory is declared by the REPORT_OUTPUT flag in the .delta_configure file. ./.icons/ This directory contains the user-specic icons used by the IRIX operating system on the Silicon Graphics workstation. Delta.icon This file contains the icon used when Delta windows are iconified. login.icon This file contains the icon used for the Delta user account on the Pandora display. Pandora is the display containing user icons when no one is logged in to the Silicon Graphics workstation. This file can be changed to reflect the user's artistic taste. ./les/ This directory contains the directories which contain unconverted user data and data in the Delta format. These directories are created by the default copy_setup script le and are used as the initial default data locations. ./les/data/ This directory contains user Delta data, and is declared by the DATA flag in the .delta_configure file. Eclipse data is uploaded to this directory from the Eclipse NMR Spectrometer. ./les/foreign_data/ This directory contains data in foreign formats (not collected on a JEOL spectrometer) that must be converted to the Delta format before processing and display. The data located here are typically JEOL GX/GSX/CPF/EX data, JEOL Alpha data, and other non-Delta data formats. The format converters use this directory as the default location for foreign data types. The GX, GSX, CPF, EX, Alpha, Varian VNMR, Bruker Aspect, and other NMR data files would be located in this directory and converted to Delta data.
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Delta System Directories, /usr/delta/
DELTA SYSTEM DIRECTORIES, /USR/DELTA/

This is the set of directories that contain the Delta programs and system default les for all Delta users.
/USR/DELTA/GLOBAL/ FILES
This directory contains the Delta executable UNIX programs, the compiled Delta Percival programs and operators, and the assignment label les. Normally this is /usr/delta/ global/, but Delta may be installed in a different location. .delta_product_key This le contains the workstation specic software key to allow Delta to run on a particular workstation. One entry in this le is required for each workstation that will use the Delta software from this directory. This le can be appended to or created by the verify program. Sample .delta_product_key file: AT-RW-RM-3O-HX -- Delta console This program is an auxiliary console for Delta. It uses the message manager to talk to Delta running on the local workstation. It functions like the input box option on the Delta console. Help output from the console program:
/usr/delta/global/console [-r -l -e -s number] -r : Reset all client ids -l : List all available servers -s : Select a server by number -e : Line editor enabled (Default) -w : Without line editor enabled -p : Initial prompt mode -n : Tell Delta which server daemon should respond to this console. -h : Connect to host.
Switches: -r Resets all message ID's used to manage message passing. -l Lists all of the copies of Delta running on a system. -s Selects a specic Delta program with which to communicate. -e Enables a line editor similar to the one on the Delta Console. -w Works without line editor enabled. -p Is the initial prompt mode. -n Tells Delta which server daemon should respond to this console. -h Connects to the host. delta This is the Delta program, by default this program executes the delta_startup.1 Percival program at runtime.
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Help output from the delta program:

usage : /usr/delta/global/delta [-hvnliwgmrs filename][-f info] Copyright 1996 JEOL USA, Inc -g : Disable Window Manager Graphics -h : Display Help -i : Disable Instrument Manager -l : Enable Local Console -n : Do Not Start -r : reset all message ids -v : Display Version -w : Disable Window Manager -x : Use mixed mode graphics (X11/OpenGL geometries) -f : Specify input info -s : Specify startup file --ogl : Force use of OpenGL graphics --igl : Force use of IRISGL graphics --x11 : Force use of X11 graphics --single : Force single-buffering --sync : Force synchonization with X server
Switches: -g Prevents Delta from drawing to the screen, but allows Delta to generate data plots. Currently works only on SGI servers. -h Prints the switch help information listed above. -i Prevents Delta from connecting to active instruments by disabling the instrument manager. -l Creates a local console to allow commands to be entered from the Percival prompt. This is similar to the yellow input box option found on the Delta Console. -n Causes Delta to load execute any other switches, typically -h or -v, and to terminate execution. -r Resets all message ID's, used to manage message passing. -v Prints the version information for Delta, program execution continues after printing. The version ag will also designate other available options, the software serial number, and the machines ID. -w Prevents Delta from doing any graphics, data plotting included. -x Uses mixed mode graphics. Use X11 for everything except geometries. -f Allows a Delta program to be started and data passed into Delta for execution at startup. -s Allows an alternate Percival startup le to be executed at beginning of the Delta program execution. --ogl Forces use of OpenGL graphics. --igl Forces use of IRISGL graphics. --x11 Force use of X11 graphics. --singl Force single-buffering for graphics. --sync Force synchronization of the X server.
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/usr/delta/global/ Files
jdc The JEOL Delta Compiler, jdc is used to compile Percival programs and operators. The input les are Percival Source (*.p) les, and the output les are Percival executable (*.1) les. Help output from the jdc program:
usage : /usr/delta/global/jdc [-swqmnreldg] file1 file2 ... Copyright 1996 JEOL USA, Inc -s -w -q -m -n -r -e -l -d -g : : : : : : : : : : Show compiling statistics display warnings Suppress all titles and output except errors Display machine code Suppress symbol tables Recompile the specified files in place Extract the source code for specified executables List operators in library Delete operators from library Global library flag
if extension is omitted from filenames, '.p' is assumed.
Switches: -s Displays the number of Percival lines compiled and the compiler speed in number of lines compiled per second. -w Displays all Percival compile time warnings. Normally these are suppressed, and appear only when a compile error is encountered in a Percival source le. -q Stops the printing of normal output except for errors encountered. -m Displays the P code that jdc generates when compiling a Percival source le. This P code is the code that Delta interprets for Percival program execution. -n Suppresses the symbol table for Percival programs. This saves on memory and loading time. The symbol tables are used for debugging Percival code. -r Recompiles a Percival program or operator to update the pointers to other Percival operators that may have changed. -e Extracts a Percival operator and creates a Percival source le. -l Lists the operators in both the local and the global Percival operator libraries. -d Deletes an operator from either the local or the global Percival operator library. -g Directs the results of jdc operations to the /usr/delta/global/ directory. send_message This program sends a message to a running copy of Delta running on the same system. It uses the message manager to talk to Delta running on the local workstation. The message can be a le name, or a program for Delta to run. Delta must be set up in advance to interpret the message. Help output from the send_message program:
./send_message [-r] [-l] [-n name] [-s number] [-f command] [message] -r : Reset all client ids -l : List all available servers -s : Select a server by number
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-n : Name of message -f : Command executed if no server found
Switches: -r Resets all message ID's and is used to manage message passing. -l Lists all copies of Delta running on a system. -s Selects a specic Delta program with which to communicate. -n Denes the name of the message for Delta operators to use. -f Denes the command to be executed if Delta is not running. nsend_message This program sends a message to a copy of Delta running on a remote system. It uses the message manager to talk to Delta running on the local workstation. The message can be a le name, or a program for Delta to run. Delta must be set up in advance to interpret the message. Help output from the nsend_message program:
./nsend_message nodename [-n name] [message] -n : Name of message
Switches: -n Denes the name of the message for Delta operators to use. verify This program generates and veries the .delta_product_key le in the /usr/ delta/global/ directory. Help output from the verify program:
verify [-h|-v|[-m]{Product-License-Key}] License management tool : -h Print this message -m Causes a license key file to be created/appended -q Dont print, just set status code -v Verify Product License Key file
Switches: -h Displays the help message. -m Creates a new .delta_product_key le or appends a new key to an existing le. -q Dont print, just set status code. -v Veries entries in the .delta_product_key le.
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upload This Bourne shell script is used to automatically upload les to a Delta workstation from the Eclipse spectrometer when an experiment is nished. Sample upload script le:
#! /bin/sh PATH=/usr/bsd:/usr/sbin:/sbin:/bin:/usr/bin:/etc if [ $# -ne 3 ]; then echo usage : $0 system targetfile destinationfile echo invoked as $0 $* exit 1 fi hostname=`hostname` directory=`dirname $3` if [ ! -d $directory ]; then mkdir -p $directory fi cd $directory result=$? if [ $result -ne 0 ]; then echo <3>upload[$$]: unable to cd to $directory >/dev/log exit $result fi output=`ftp -n $1 2>&1 <<-! | head -1 user anonymous ${hostname}@ binary get $2 upload$$ ! ` test -z $output result=$? if [ $result -ne 0 ]; then echo <3>upload[$$]: upload of $3 FAILED : $output >/dev/log exit $result fi mv -f upload$$ `basename $3` result=$? if [ $result -ne 0 ]; then echo <4>upload[$$]: rename of $directory/upload$$ to $3 FAILED >/dev/log else echo <6>upload[$$]: upload of $3 succeeded >/dev/log fi exit $result
global_percival_operator_library.1 This is the global library le for compiled Percival operators. Additions and deletions to this library are controlled by the -g option on the JEOL Delta Compiler, jdc. *.1 les These les are the compiled Percival programs that Delta uses for execution. Percival programs are placed in the /usr/delta/global/ directory when the -g switch is used.
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assignment.* les The les, assignment.groups, assignment.residues, and assignment.types are used as the labels in the spreadsheet, and on plots. Do not change the text in these les! Your assignments will not be correct if the body of these les is changed after assignments have been made. You can make additions to the end of these les if additional assignment labels are required. Characters preceded by a ^ are converted to Greek. Data File Programs and Format Converters These programs are used to convert, to export, to list information about, and to x damaged Delta data les. convert This program is the standard data format converter for JEOL's GX, GSX, CPF, and EX NMR data files. This program will automatically convert 1D NMR data and 2D complex by real data without any switches. It will also convert 2D complex by (real, complex or tppi) data, and 3D complex by (real, complex or tppi) by (real, complex or tppi) data when the appropriate switches, described below, are used. To redirect the output to a file with a name different from the standard name use the -o switch. This must be the last switch and be immediately followed by the new filename and the truncated *.gx* filename. Converter Help: convert convert [global_switches] {outswitch}+
-intype
{inswitch}+
-outtype
Convert v1.10 Copyright (C) 1997-1998 JEOL libRX 1.5 Copyright (C) 1995, 1996 Tom Lord This program is supported at following data format: Import Vendor Product Input Max dimension -------------------------------------------------------------------------------------JEOL GX FID 2 JEOL GSX FID 2 JEOL CPF FID 2 JEOL EX FID 2 JEOL ALPHA FID 4 JEOL Lambda FID 3 JEOL Alice FID 2 JEOL Eclipse/ECP/Delta FID/Spectrum 6 JEOL JEOL Generic FID/Spectrum 6 JEOL CMX FID 2 Varian INFINITY FID 2 Varian VXR FID 3
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Varian UNITY Bruker AC Bruker AMX/DMX Acorn NMR NUTSF Galactic Grams/3 MSI Felix --JCAMP-DX 5.0
FID FID FID ID/Spectrum FID/Spectrum FID/Spectrum FID/Spectrum
3 3 3 2 2 3 3
Export Vendor Product Output Max dimension ----------------------------------------------------------------------------------JEOL GX FID 2 JEOL Alice FID 2 JEOL Eclipse/ECP/Delta FID/Spectrum 6 JEOL Generic FID/Spectrum 6 AcornNMR NUTS FID/Spectrum 2 Galactic Grams/32 FID/Spectrum 2 MSI Felix FID 3 NMR Pipe FID 3 JCAMP-DX 5.0 FID/Spectrum 3 Usage convert [global_switch] -intype {inswitch} -outtype {outswitch} global_switch : -help [intype outtype] : display help -server [serverID] : information server ID -quiet : quiet mode (no message display) intype -delta -gx -alpha -lambda -alice -jeol_generic -cmx -vxr_unity -ac -amx -cdff_nuts -galactic -felix -jcamp inswitch
: JEOL Eclipse/ECP/Delta : JEOL GX/GSX/CPF/EX : JEOL ALPHA : JEOL Lambda : JEOL Alice : JEOL Generic format : JEOL CMX / Varian INFINITY : Varian VXR/UNITY : Bruker AC : Bruker AMX/DMX : Acorn NMR NUTS : Galactic Grams : MSI Felix : JCAMP-DX 5.0 format
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-le [lename] : input le (or directory) name -separate : use JEOL GX/GSX/CPF/EX 2D phase sensitive data ..... others.(See help of intype) outtype -delta -gx -alice -jeol_generic -cmx -cdff_nuts -galactic -felix -nmrpipe -jcamp
: JEOL Eclipse/ECP/Delta : JEOL GX/GSX/CPF/EX : JEOL Alice : JEOL Generic format : JEOL CMX / Varian INFINITY : Acorn NMR NUTS : Galactic Grams : MSI Felix : NMR Pipe : JCAMP-DX 5.0 format
outswitch -le [lename]: output le name Examples: convert -alpha -le GLUCOSE_HSQC.NMF -delta -le glucose_hsqc This command would convert from ALPHAs le GLUCOSE_HSQC.NMF to ECPs le glucose_hsqc. Examples: convert -Ra -Ib -ir -c2 -o gramacidin gram This would convert the les 'grama.gxd' and 'gramb.gxd' into the le 'gramacidin' using the irradiation frequency as the observation frequency. convert -c2 -c3 4 EXP This would convert the les 'EXPRR1.GXD', 'EXPRI1.GXD', 'EXPIR1.GXD', 'EXPII1.GXD', 'EXPRR2.GXD', etc. into 'exp' using the observation frequency. xup This program will attempt to x problems with the header of a Delta data le. These problems sometimes occur when Delta crashes with les open.
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list_header This program will list the header sections of a Delta data file. Help output from the list_header program:
/usr/delta/global/list_header : [-+][acfhlp] files... Use - (+) to turn off (on) annotations, condensed format, full header, history, lists, parameters Use - (+) alone to turn off (on) all
Switches: + Lists all sections or a particular listing when used with one of the switches below. - Prevents all or a particular section from being listed. a Lists any annotations present in the data set. c Lists all dimensional information on a single line. f Lists the full header information. h Lists the processing history of the file. l Lists the non-ranged lists in the file header, for example t1 value lists. p Lists acquisition parameters. Icons & Logos These les are icons and logos used by Delta for Percival tools and plots. delta_screen.rgb This file is displayed on a system before the demo license key expires and does not have a valid .delta_product_key file. global.rgb This file is used as a push button in the standard file selection window. It initially selects a global directory for the file type being opened or saved. jeol.eps This file is used as a logo on plots. It is an Encapsulated Postscript (EPS). You may make your own logo with a standard word processor by printing to an EPS file and copying it to /usr/delta/global/ with the filename jeol.eps. This logo will appear only on postscript printers. local.rgb This file is used as a pushbutton in the standard file selection window. It initially selects a local directory for the file type being opened or saved.
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spinning_delta#.RGB info These les make up the Delta icon with the JEOL USA logo. ding.aifc This is the default sound file the bell operator will play.
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/usr/delta/global/ Directories
/USR/DELTA/GLOBAL/ DIRECTORIES
/usr/delta/global/automation/ This directory contains les required for automation. This directory will be omitted or empty if Delta was installed without machine control. usr/delta/global/experiments/ This directory and its sub-directories contain the standard JEOL-supplied experiments that are globally accessible to all users. This is the initial directory for JEOL-supplied global experiments. This directory is will be omitted or empty if Delta was installed without machine control. /usr/delta/global/help/ This directory contains the les used for the JEOL Delta Help system. *.html Files These files form the JEOL Delta Help system. *.gif Files Image files for the JEOL Delta Help system. usr/delta/global/process_lists/ This directory contains standard processing lists that are globally accessible to all users. The standard automation also uses some of the lists for data processing. usr/delta/global/templates/ This directory contains viewer, automation, and plotter layout templates that are globally accessible to all users. *.pmt These types of les are Presentation Manager templates. *.eps These types of les are encapsulated Postscript les for the Presentation Manager. *.auto These types of les are Automation templates. .delta_automation.auto The default JEOL supplied Automation template. This le contains many commonly used experiments.
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/USR/DELTA/SETUP/
This directory contains the standard les used by the Delta user account, the printers, and other system conguration les for Delta. Files beginning with dot.filename are renamed .filename and do not appear in standard le listings, such as ls -l. copy_setup script le This shell script will create the standard Delta user directories, and copy standard UNIX conguration les to the user's root directory. Warning: this script overwrites existing les in the users directories. Files for USER Setup: Delta.icon This file contains the icon used when Delta windows are iconified. It is copied to the .icons/ directory. .auxchestrc This file contains descriptions for the toolchest found in the upper left of the screen. For more information, type man toolchest in an X terminal shell window. .cshrc This is a file used by the shell that sets UNIX environment variables and creates a standard set of aliases for Delta. Aliases are convenient shortcuts for using Delta and for navigating between the directories that Delta uses. This file is run each time an xwsh terminal window is created. The aliases generated by this file can be viewed by typing alias in an X terminal shell window. .delta_congure This file is the standard Delta configuration file. It is described in detail in the Delta User Account Section. delta_drop Copy and rename this command to the name of a Delta tool (such as data_slate) and place its icon on the desktop. You can then bring up the tool by dropping a data le on it. Delta will start if it is not running. .delta_parameter_list This file is the standard Delta parameter list file. It contains user-selected parameters that appear in the parameter list tool and on parameter plots. .grosview This file contains configuration information for gr_osview, a system usage monitoring tool. The gr_osview program can be started by typing gr_osview in an X terminal shell window, or by selecting the system usage button in the toolchest.
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/usr/delta/setup/
.login This file is run when the user logs in. The .login file sets the search path for user-entered commands, and sets the environment variables used by UNIX. .icons/login.icon This file contains the icon used for the Delta user account on the Pandora display. Pandora is the display containing user icons when no one is logged into the Silicon Graphics workstation. This file can be changed to reflect the user's artistic taste. pull This file is a shell script used to move files from a JEOL GX/GSX/CPF/EX data system to the SGI system. The PDP system needs to have ftp running on it. copy_setup Copies the Delta setup and conguration les to the users login account directories. Use caution. This will remove the users current login settings. .delta_congure_root This file is similar in structure to the .delta_configure file, but is only used by the root account. get_spectrometers Prints out a list of spectrometers available on the network. kermit Kermit is used with the shim robot. This is copy of kermit-C from Columbia University. All rights are reserved, and this copy of kermit is being supplied at no charge. X keyboard les These files used for X Windows emulators: exceed_delta.kbf & wrq_delta.dmp Keyboard mapping les for PC computers running Exceed or Reections (X Windows server applications) under Microsoft Windows (r). exodus_delta.bin Keyboard mapping les for Macintosh computers running Exodus, an X Windows server application.
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DELTA PERCIVAL SOURCE FILES

/usr/delta/source/ This directory contains the source for the JEOL supplied Percival programs and operators. *.p Files These files contain the standard Delta Percival source code for the Percival programs and operators used by Delta.
ECLIPSE FILES FOR ACQUISITION SYSTEM

/usr/delta/eclipse/ This directory contains the programs and configuration files used on the Eclipse NMR Spectrometer and on Delta-Upgrade systems. This directory will be omitted or empty if Delta was installed without machine control. backup_spectrometer This script file is used to backup the Eclipse Acquisition system configuration files from the acquisition system to the workstation. restore_spectrometer This script file is used to restore the Eclipse Acquisition system configuration files from the workstation to the acquisition system. update_spectrometer This script file is used to update the Eclipse program files on a SGI V35 based Eclipse acquisition system running a version of SGI IRIX. /usr/delta/eclipse/probes/ This directory contains the initial probe configuration files for the Eclipse NMR probes. usr/delta/eclipse/dist/ This directory contains Irix install files for SGI Indy based acquisition systems Running Irix V5.3 or higher.
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Delta Configuration Files
DELTA CONFIGURATION FILES

.delta_congure This is the primary conguration le containing parameters to adjust the behavior of the Delta user environment. This le must reside in the user's root directory. The selections in the .delta_configure le are managed by the Delta Console Preferences Tool. This le must be in the root (login) directory for the user account. Entries that begin with -- are comments and are not used as conguration parameters for Delta. Each entry must be on one line. The ~ appearing in a preference entry will be substituted with the user's root directory path name. .delta_configure File Entries for the Preferences Tool: Note: entries that have a * require Delta to be restarted to be operative. Note also that this list is alphabetized by the Preference Tool page, and that the name as it appears on the page is rst, followed by the name that appears in the .delta_congure le, and when you select this title with the mouse.
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Personal Page: Author, AUTHOR The name used by the Delta software and stored in data les collected by the user. This name designates the creator of the experiment data les. The default is Delta Account. Browser, BROWSER The full path (i.e. /usr/bin/netscape/) of the html browser used for help. Leave blank unless help complains it cannot nd Netscape. Editor, EDITOR The Unix command used to invoke a text editor to use for editing les. If this entry does not exist, or does not refer to an existing program, then the Percival CM~EDIT command will not function. The default is "/usr/sbin/jot", a standard editor supplied by Silicon Graphics. Email, EMAIL The E-mail address of the author. Instrument, DEFAULT_INSTRUMENT The internet address of the spectrometer to auto-connect to when the Spectrometer Control Tool is opened. There is no default for this parameter. Password, PASSWORD A password used for connecting to an Eclipse NMR spectrometer as the console. If this password matches the password in the .delta_configure file on the Eclipse Acquisition computer, the user is automatically connected as console. If the password is supplied on the Spectrometer Control Tool, then the user will be connected in Console Mode when the Connect button is pressed. There is not a default password. Site, SITE This could be the name of a company or organization. There is no default for this parameter. Startup Console, DELTA_CONSOLE * The name(s) of a Percival program(s) that will be run when Delta is started. The default is "master_console". Balloon Help, AUTO_HELP_ON ON/OFF. When ON, and the mouse cursor is held still over a widget, for a certain amount of time, balloon help will appear automatically. The default is ON. Balloon Help Delay, AUTO_HELP_TIME The number of seconds to wait over a widget before balloon help automatically
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pops up. The default wait time is 1[s] (1 second). Balloon Help Time, HELP_WAIT_TIME The number of seconds automatic pop-up help is visible. Setting this value to zero will make balloon help visible as long as the mouse is over the widget. The default wait time is 1[s] (1 second). Button Press Freq., STILL_PRESSED_TIME The time (in seconds) when a mouse button is held for a Percival message to be sent that informs Delta that the mouse button is still pressed. The default is 0.1[s] (1/10 second). Double Click Rate, DOUBLE_CLICK_TIME The maximum length of time (in seconds) allowed to pass in which two mouse clicks must occur to constitute a double click. The default is 0.5[s] (1/2 second). Drag Delay, DRAG_WAIT_TIME The number of seconds to wait over a widget with the third mouse button pressed before the drag-and-drop dragon disappears. When the third mouse button is pressed, the mouse cursor changes to the Drag-and-Drop icon. The defaults is 0.5[s] (1/2 second). Conrmation, CONFIRMATION ON/OFF. When ON, the user is prompted for conrmation before certain potentially harmful actions. The default is ON. Simple Mode, SIMPLE_MODE ON/OFF. A general parameter that is global to all tools with a simple mode of operation. The default is OFF. File/Directory Page: Note: ~ in the directory paths indicate the users home directory. Data, DATA The directory (~/files/data/) containing user-generated Delta data, declared by the DATA flag in the .delta_configure file. Eclipse data is uploaded to this directory from the Eclipse NMR Spectrometer. It is the default local directory for Delta data files. Executable, EXECUTABLE The directory (~/delta/library/) for Percival executable les. Experiment, EXPERIMENT The directory (~/delta/experiments/) containing user-written experiments
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for the Eclipse NMR Spectrometer. This directory is declared by the EXPERIMENT flag in the .delta_configure file. It is the default local directory for Delta experiment files. Foreign Data, FOREIGN_DATA The foreign data directory (~/files/foreign_data/) containing data not collected on a JEOL spectrometer that must be converted to the Delta format before processing and display. Gamma, GAMMA Reserved for future use. The local directory for gamma les. Global, GLOBAL The global directories containing the Delta executable UNIX programs and the compiled Delta Percival programs and operators. Warning! Do not change this value inside the Preferences Tool. It will cause Deltas internal operators to stop functioning properly. Instrument, INSTRUMENT Instrument information directory (~/delta/instrument/) containing user shim les and other related user instrument les. Library, LIBRARY The library directory (~/delta/library/) specifying the location of compiled Percival operators (.l les) and the local library le. PM Template, PM_TEMPLATE The Presentation Manager directory. There is no default for this preference. Process List, PROCESS_LIST The directory (~/delta/process_lists/) specifying the location of the user's process lists. Report Output, REPORT_OUTPUT The directory (~/delta/reports/) specifying the location for output. Source, SOURCE The directory (~/delta/p_files/) specifying the location of the user's Percival programs (.p les). Template, TEMPLATE The directory (~/delta/templates/) specifying the location of templates for certain Delta tools. Global Data, GLOBAL_DATA
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The global directory where most of the Delta les exist. Global Executable, GLOBAL_EXECUTABLE. The global directory for Percival executable programs. Global Experiment, GLOBAL_EXPERIMENT The global directory for experiment les. Global Foreign Data, GLOBAL_FOREIGN_DATA The global directory containing data in foreign formats (not collected on a JEOL spectrometer) that must be converted to the Delta format before processing and display. The data located here are typically JEOL GX/GSX/CPF/EX data, JEOL Alpha data, and other non-Delta data formats. Global Gamma, GLOBAL_GAMMA Reserved for future use. Global Instrument, GLOBAL_INSTRUMENT The global directory containing user Shim les and other related user instrument les. This directory is declared by the INSTRUMENT ag in the .delta_configure le. Global Library, GLOBAL_LIBRARY The global directory specifying the location of compiled Percival operators (.1 les) and the local library le. Global Process List, GLOBAL_PROCESS_LIST The global directory specifying the location of the user's process lists. Global Report Output, GLOBAL_REPORT_OUTPUT The global directory specifying the location for reports. This is the default directory for Delta output les and messages. Global Source, GLOBAL_SOURCE The global directory specifying the location of the user's Percival source programs (.p les). Global Template, GLOBAL_TEMPLATE The global directory specifying the location of templates used for certain Delta tools.
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Printer/Plotter Page: Printer, PRINTER The name of the default printer (e.g. "lj4"). This printer is used by the printer icon on many Delta tool bars. The name used must match the name found in the IRIX Print Manager Tool. There is no default for this preference. Color Printer, PRINTER.COLOR ON/OFF. If ON, plots will be printed in color on color printers. This preference has no effect for BW printers. The default is OFF. Printer Orientation, PRINTER.ORIENTATION PORTRAIT/LANDSCAPE. Indicates the default plot orientation. The default is LANDSCAPE. Printer Paper Size, PRINTER.PAPER_SIZE A/B/C/D/E/LEGAL/A0/A1/A2/A3/A4. A string that indicates the paper size loaded into the default printer. The default is A. Peak/Integral Paper Size, PEAK_INTEGRAL_PAPER_SIZE A/B/C/D/E/LEGAL/A0/A1/A2/A3/A4. This value indicates paper size to use when printing peak and integral information. The default is A. Printer Tessellate, PRINTER.TESSALATE An integer between 1 and 64 that informs the printer of the number of triangles to break a surface into for plotting. The higher the number, the better the resolution of the data, but the more time it takes to compute. This value species the neness of polygon size and color shading when plotting 2D or 3D spatial geometries. Lower numbers create coarser shade differences, but are faster and require less memory. The defaults is 8. Plot Options, PRINTER.OPTIONS Characters that correspond to the features of a plotted geometry that effect the geometry features that are displayed on the plot. There is no default for this parameter. Print JEOL Logo, PRINTER.JEOL_ICON ON/OFF. If ON, then when data les are sent to be plotted, the JEOL icon (stored in jeol.eps) is plotted with the data. This determines whether the plot should include the JEOL icon. The default is OFF. Print Parameters, PRINTER.PLOT_PARAMS ON/OFF. When ON, the data les parameters are plotted with the data. The default is OFF. Parameters Location, PRINTER.LOCATION
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LEFT/BOTTOM/RIGHT/TOP. Indicates where the data le parameters are to appear on data le plots. The default is LEFT. Plot Border, PLOT_BORDER ON/OFF. When ON, a thin border line is displayed around plots. The default is ON. Geometry: Negative Contour Grey, GEOMETRY.NEG_CONTOUR_GREY ON/OFF. When ON, the negative peaks will be displayed in light gray (not black) when plotting a 2D contour. The default is ON. Plot Dialog, PRINTER.DIALOG ON/OFF. When printing from Process 1D or Data Slate and this preference is ON, then a dialog box will appear allowing the user to set some printer conguration parameters before sending the plot to the printer. The dialog box will time-out, and send the plot in 20 seconds if the printer parameters are not modied. The default is ON. PostScript Emulator, PRINTER.POSTSCRIPT_EMULATOR A boolean. Normally it is set to OFF, but if your printer is a PostScript emulator and does not print PostScript les very well (long delays or errors duirng printing), then you may want to set this to ON. Lines Per Page, PRINTER.LINES_PER_PAGE Defaults to FALSE. Can be any integer between 20 and 132. The number of lines per page that the printer can print standard text les. Plot Dash n Where n = 1 - 8. When plotting overlaid data, each data set will be shown with the dash pattern specied. The pattern is used cyclically. Length of 1 is roughly 1 millimeter. Data Page: All Overlays, GEOMETRY_OPTIONS.ABR_FULL ON/OFF. When ON, all overlays (le names and shadow dimensions) will be displayed in the upper left corner of a geometry. When OFF, only the lename and shadow dimension of the current slot is displayed. The default is OFF. Annotations, GEOMETRY_OPTIONS.ANNOTATION ON/OFF. When ON, annotations will be visible on geometries. The default is ON. Comment, GEOMETRY_OPTIONS.COMMENT ON/OFF. When ON, the le comment will be displayed in the upper left corner of geometries. The default is OFF.
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Contour Line Check, LEVEL_TOOL.LINE_COUNT_CHECK ON/OFF. When ON, the contour line limit will be checked when drawing contours. When OFF, the limit is not checked and it may cause problems when computing contours below the peak threshold level. The default is ON. Contour Line Limit, LEVEL_TOOL.LINE_COUNT_LIMIT The maximum number of line segments allowed to draw a contour line. If the number of line segments needed to draw a particular contour line exceeds this limit, then the entire contour level will not be displayed. If Contour Line Check is set to OFF, this limit is not checked and may cause problems when computing contours below the peak threshold level. The default is 5000. Cursor, GEOMETRY_OPTIONS.CURSOR ON/OFF. When ON, geometry cursors are displayed on geometries and may be created or destroyed. The default is OFF. Data, GEOMETRY_OPTIONS.DATA ON/OFF. When ON (the default), data is visible in the geometry. When OFF, the data is hidden. Data Points, GEOMETRY_OPTIONS.UNDERLINE ON/OFF. For 1D les only. When ON, a small white square will be displayed around each data point in the le. The default is OFF. Deconvolve, GEOMETRY_OPTIONS.DECONVOLVE ON/OFF. When ON, the primitive theoretical curves (deconvolutions) of the data peaks displayed in geometries over the data if it has been computed. The default is OFF. Deconvolve Sum, GEOMETRY_OPTIONS.DECONVOLVE_SUM ON/OFF. When ON, the sum of the deconvolved peaks is displayed in geometries over the data if the deconvolutions have been computed. The default is OFF. Deconvolve Unselected, GEOMETRY_OPTIONS.DECONVOLVE_UNSELECTED ON/OFF. When OFF, the deconvolution curves are only displayed over the peaks which are selected. Deconvolutions must be computed. The default is ON. Draw: Backface, LEVEL_TOOL.BACKFACE ON/OFF. When ON, the back faces of 3D and higher data sets are displayed. Otherwise, only data facing the viewer will be displayed. The default is ON. Draw: Blend, LEVEL_TOOL.BLEND ON/OFF. When ON, the pixels representing the data are displayed after blending color with surrounding pixels. The result is a smoother, thicker data curve. The default is ON.
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Draw: Dither, LEVEL_TOOL.DITHER ON/OFF. When ON, color is approximated with a dithering technique. The default is ON. Draw: Double Side, LEVEL_TOOL.2SIDE ON/OFF. When ON, both sides of the data are displayed. This will cause a seethrough effect for 3D and higher data sets. The default is OFF. Draw: Gradation, LEVEL_TOOL.GRADATION ON/OFF. When ON, the colors dened for Data Color are used for the contour colors in 2D data sets. Otherwise, data color for the current slot value is used. The default is OFF. Draw: Smooth, LEVEL_TOOL.SMOOTH ON/OFF. When ON, the data curve is smoothed with the anti-aliasing technique. The result is a less ragged data curve. The default is ON. Draw: Solid, LEVEL_TOOL.SOLID ON/OFF. When ON, colors are displayed at full brightness for all levels. When OFF, colors are modied by the bias set in the Level Tool -- lower levels appear dimmed. The default is OFF. Draw: Texture, LEVEL_TOOL.TEXTURE ON/OFF. When ON, 2D and higher data sets when displayed in surface or mesh mode will be displayed using the level colors. The default is OFF. File Name, GEOMETRY_OPTIONS.INTEGERS ON/OFF. When ON, the lename(s) of the data le(s) will be displayed in the upper left corner of geometries. The default is OFF. Geom Border, GEOMETRY_OPTIONS.PLOT_GEOM_BORDER ON/OFF. When ON, a thin border is displayed around geometries when plotted. The default is OFF. Grid, GEOMETRY_OPTIONS.GRID ON/OFF. When ON, a grid will be displayed in the datazone area of geometries. The default is ON. Integrals, GEOMETRY_OPTIONS.INTEGRATION ON/OFF. When ON, integrals will displayed over the data in geometries. Integrals must be calculated or created. The default is OFF. Integral Normal, INTEGRAL_NORMAL The value to which the largest integral will be normalized. The default is 1. Integral Precision, INTEGRAL_PRECISION
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The number of decimal points to display in the integral value(s). The default is 5. Integral Tails, INTEGRAL_TAIL_MULT A multiplier indicating the desired length of the ends of integrals. A larger value will make the integral appear wider. The default is 1. Integral Value, GEOMETRY_OPTIONS.INTEGRATION_VALUE ON/OFF. When ON, integral values will be displayed next to the end of all integral curves. The default is ON. Line Hiding, GEOMETRY_OPTIONS.LINE_HIDING ON/OFF. For nD stack displays only. When OFF, all data vector lines are displayed completely. When ON, vectors in front in stack plots will occlude other vectors behind them, depending on the user's viewing angle. The default is OFF. Note: Line hiding is computationally intensive and makes for much slower refresh drawing and refresh rates. Peak, GEOMETRY_OPTIONS.PEAK ON/OFF. When ON, peak positions will be displayed, and peaks can be created and manipulated. Their axial positions will be indicated in the ruler or above the data. The default is OFF. Peak Above, GEOMETRY_OPTIONS.PEAK_ABOVE ON/OFF. When ON, peak positions will be displayed above the peaks rather than in the X ruler. Peak locations will marked by a white line above the peak in the datazone area. The default is OFF. Peak Integrals, GEOMETRY_OPTIONS.PEAK_INTEGRATION ON/OFF. When ON, integrals are displayed in grey for each peak, and can be manipulated for peak groups. Integral information must exists in the data le for the integrals to be visible. The default is OFF. Peak Precision, PEAK_PRECISION Values = 1..12. This is the number of decimal places to display for the peak pick values. The default = 5. Max Peaks Allowed, MAX_PEAKS_ALLOWED The maximum number of peaks that will be found with the auto-analyze function when an auto peak pick is performed. The default is 5000 peaks. Plot Transparent, GEOMETRY_OPTIONS.PLOT_TRANSPARENT ON/OFF. When OFF and the widgets are plotted, what is behind the widget will be obscured by the top widget. When ON, anything previously plotted behind the widget will be visible. The default is ON. Regions, GEOMETRY_OPTIONS.REGIONS
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ON/OFF. When ON, regions can be created and manipulated in geometries. The default is OFF. Scale Solvent, GEOMETRY.SCALE_SOLVENT ON/OFF. When ON, and there is a solvent peak in the data le, the solvent peak will not be included in the calculation of vertical extent in the data. When OFF, all data points are included in this calculation. The default is OFF. Sequence, GEOMETRY_OPTIONS.SEQUENCE ON/OFF. When ON, sequence analysis information will be displayed in geometries. The default is OFF. Sequence Marker, GEOMETRY_OPTIONS.SEQUENCE_MARKER ON/OFF. For nD data sets displayed in contour mode. When ON, lines are displayed marking the center of each peak. The default is OFF. Shadow Dimensions, GEOMETRY_OPTIONS.DECIMALS ON/OFF. When ON, shadow dimension(s) of each le in geometries are displayed in the upper left corner of the datazone area. The default is ON. Statistics, GEOMETRY_OPTIONS.STATISTICS ON/OFF. When ON, the baseline, +/- threshold, and noise lines are displayed for the currently selected data in the geometry. The default is OFF. Positive Levels, GEOMETRY_OPTIONS.POS_LEVELS ON/OFF. When OFF, the positive levels will not be visible in 2D contour geometries. The default is ON. Negative Levels On, GEOMETRY_OPTIONS.NEG_LEVELS ON/OFF. When OFF, negative levels will not be visible in 2D contour geometries. The default is ON. Geometry Page: Geometry: Hints, GEOMETRY_HINTS_ON * ON/OFF. When ON, the geometry selectively displays appropriate features for the current cursor mode. When entering a cursor mode, certain features may be turned on or off. When the cursor mode changes, the geometry features are updated to reect the defaults for the new mode. When OFF, the geometry features are not changed with the cursor mode. The default is ON. Geometry: Persistent Mode, GEOMETRY.HOLD_FEATURE ON/OFF. When ON, features that are normally turned off on geometries when the user switches cursor modes will stay on. For example, go into Peak mode (peaks turn on); go into Integration mode (integrals turn on, and peaks stay on). If OFF, then peaks would turn off in this example. The default is OFF.
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Geometry: Peak Unit, GEOMETRY.PEAK_UNIT Species the unit that the peaks will be displayed in for geometries that have peak information. Some tools allow the peak units to be changed via the pull-down menus. The default is to display the same units that are the base units of the data.
Geometry: Rotation, GEOMETRY.ROTATION ROTATE/NOROTATE/AUTO_ROTATE. Species the initial type of rotation of geometries. NOROTATE indicates that the X axis is always horizontal. ROTATE indicates that the X axis is always vertical. AUTO_ROTATE indicates that the X axis will be displayed on the longer side of the geometry widget space. The default is "AUTO_ROTATE". Cursor Mode, DEFAULT_CURSOR_MODE * ANNOTATION/CURSOR/DATA/INTEGRATION/MOLECULE/OFFSET/ PEAK/PICK/REFERENCE/REGIONS/PIP/ZOOM. The default cursor mode set when Delta starts. The default is "DATA". Border, GEOMETRY_OPTIONS.BORDER ON/OFF. When ON, a light blue border is displayed around each PIP window. The default is ON. Center, GEOMETRY_OPTIONS.CENTER ON/OFF. When ON, all lines of text are centered on a widget. For a list box, long lines of text are wrapped if they are too long to display completely. The default is OFF. Cursor Tool, GEOMETRY_OPTIONS.SHOW_CURSORS ON/OFF. When ON, the cursor tool will be available on geometries. The default is ON. Cursor Tool Open, CURSOR_TOOL_OPEN ON/OFF. When ON, the cursor tool on the geometry widget will be displayed full size. When OFF, the tool will be displayed in its closed state. The default is OFF. Enable, GEOMETRY_OPTIONS.ENABLE ON/OFF. When ON, the geometry accepts user interaction. When OFF, the widget appears 'grey' and does not accept user interaction. The default is ON. Freeze Slot, GEOMETRY_OPTIONS.FREEZE_SLOT ON/OFF. When ON and the geometry is connected to a spectrometer, the data in slot 1 is left unchanged, and subsequent acquisitions are sent to slot 2. The default is OFF. Geom Windows, GEOMETRY_OPTIONS.GEOM_WINDOWS ON/OFF. When ON, a light blue border is displayed around areas for which there
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is a PIP window active. The default is ON. Interactive, GEOMETRY_OPTIONS.INTERACTIVE ON/OFF. When ON, the widget will react to keyboard and mouse events. When OFF, user interaction is ignored. The default is ON. Molecule Borders, GEOMETRY_OPTIONS.MOLECULE_BORDER ON/OFF. When ON, a square border will be visible around all molecules in geometries. The default is ON. Molecule Titles, GEOMETRY_OPTIONS.MOLECULE_NAME ON/OFF. When ON, the molecule name will be visible in the upper-left corner of the molecule window as well as any text the user has added. The default is OFF. Molecule Windows, GEOMETRY_OPTIONS.MOLECULES ON/OFF. When ON, molecule windows will be visible. The default is ON. Atom Numbers, GEOMETRY_OPTIONS.ATOM_NUMBERS ON/OFF. When ON, the atom numbers will be displayed for every atom in the molecule(s). The default is OFF. Atom Select Numbers, GEOMETRY_OPTIONS.ATOM_SEL_NUMBERS ON/OFF. When ON, the atoms numbers will be displayed only for the atoms which are selected. If the Atom Numbers preference is set to ON, then this preference will have no effect. The default is OFF. Atom Sequence, GEOMETRY_OPTIONS.ATOM_SEQUENCE ON/OFF. When ON, the selected atom numbers will be displayed with the sequence information above the peak for which the atom is connected. The default is OFF. Note: Sequence information must be turned on. No Auto Contour, GEOMETRY_OPTIONS.NOAUTOCONTOUR ON/OFF. When ON, les added to a geometry will NOT be auto-contoured. The default is OFF. No Zooming, GEOMETRY_OPTIONS.NOZOOM ON/OFF. When ON, zooming and related functions will not function. The default is OFF. Overlay Offset X, OVERLAY_OFFSET_X The overlay offset on the X ruler (in percentage). A value of zero will not offset the overlay at all. Negative numbers will offset the data to the left. Positive data will offset the data to the right. A percentage in the range of -100 to 100 informs the geometry to shift the data in slots greater than 1 on the X axis.
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Thus each slot is shifted (slot - 1) * offset percent. The default is 0. Overlay Offset Y, OVERLAY_OFFSET_Y The overlay offset on the Y ruler (in percentage). A value of zero will not offset the overlay at all. Negative numbers will offset the data down. Positive numbers will offset the data up. A percentage in the range of -100 to 100 informs the geometry to shift the data in slots greater than 1 on the X axis. Thus each slot is shifted (slot - 1) * offset percent. The default is 0. Overview, GEOMETRY_OPTIONS.OVERVIEW ON/OFF. When ON, zoom functions are disabled. Performing a zoom will create a region instead. The default is OFF. Peak Threshold On, PEAK_THESHOLDS_ON ON/OFF. When ON, peaks will not be able to be created or selected below the threshold level. An automatic peak-pick will only generate peaks that meet or exceed the threshold. The default is OFF. Perspective, GEOMETRY_OPTIONS.PERSPECTIVE ON/OFF. When ON, multi-dimensional data sets are displayed with the perspective of 3D space -- data is drawn within a frustum. Otherwise, a cube is used for the data display area. The default is ON. PIP Font Factor, PIP_FONT_FACTOR A number representing the scaled font size of a Picture-In-Picture geometry in relation to the parent's font size. The default is 0.5. Plot All Text, GEOMETRY_OPTIONS.COLUMNAR ON/OFF. Used for plotting labels. When ON, text on labels is truncated to 40 characters and formatted into columns. The default is OFF. Process FID, GEOMETRY_OPTIONS.PROCESS_FID ON/OFF. When ON, and the geometry is connected to a spectrometer that is currently collecting data, the data displayed will be processed with a Hamming apodization function and an FFT domain transfer function applied. The default is OFF. Region Manipulation, GEOMETRY_OPTIONS.NOREGIONS ON/OFF. When ON, regions cannot be created or manipulated in 3D geometries, but will still be visible. The default is OFF. Stereo, GEOMETRY_OPTIONS.STEREO ON/OFF. When ON, nD data in the geometry will be drawn in stereo vision to be viewed with special glasses. The default is OFF. This feature is not currently supported.
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Toggle Slot, GEOMETRY_OPTIONS.TOGGLE_SLOT ON/OFF. When ON, and the geometry is connected to a spectrometer that is collecting data, the data will be displayed alternately in slots 1 and 2. The default is OFF. Track Position, GEOMETRY_OPTIONS.TRACK_POSITION ON/OFF. Used only for Frame widgets. When ON, all Frame widgets whose parent is the Screen will record information about its current size and position on the desktop. If the window is closed and reopened, it will automatically appear at the same position with the same dimensions. The default is OFF. Transparent X Ruler, GEOMETRY_OPTIONS.TRANSPARENT_XRULER ON/OFF. When ON, the X ruler markers and grid lines are not displayed. The default is OFF. Transparent Y Ruler, GEOMETRY_OPTIONS.TRANSPARENT_YRULER ON/OFF. When ON, the Y ruler markers and grid lines are not displayed. The default is OFF. Transparent Z Ruler, GEOMETRY_OPTIONS.TRANSPARENT_YRULER ON/OFF. When ON, the Z ruler markers and grid lines are not displayed. The default is OFF. X Ruler, GEOMETRY_OPTIONS.X_RULER ON/OFF. When ON, the X ruler is displayed. Y Ruler, GEOMETRY_OPTIONS.Y_RULER ON/OFF. When ON, the Z ruler is displayed. Z Ruler, GEOMETRY_OPTIONS.Z_RULER ON/OFF. When ON, the Z ruler is displayed. Positive Levels, LEVEL_TOOL.COMPUTE_LEVELS.POS A number to indicate the positive levels in the data geometry which are initially computed and displayed for a new data set. If all levels are off, Level Tool default settings will be displayed. For example to have only levels 1, 2, and 4 on, one would set this value to be 20 + 21 + 23 = 11. The default is 0. Negative Levels, LEVEL_TOOL.COMPUTE_LEVELS.NEG A number to indicate the negative levels in the data geometry which are initially computed and displayed for a new data set. If all levels are off, Level Tool default settings will be displayed. For example to have only levels 4, 7, and 10 on, one would set this value to be 23 + 26 + 29 = 584. The default is 0.
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Cursor Page: This page has toggles that allow the user to redene the alternate cursors for each cursor mode. The .delta_congure preference has the form, ALT_CURSOR.XXX, where XXX is the name of each cursor mode. Changes made to these preferences will only take effect once Delta is restarted. Colors Page: These values indicate default colors for Delta Tools and Delta Data. The colors can be selected from the colors dened by X-windows. A list of the colors available can be found in the Preference Tool, the Widget Editor, or by typing colorview -browse at the command prompt in an xwsh terminal shell window. foreground, FOREGROUND * Black is the default color for widget foregrounds. background, BACKGROUND * Grey50 is the default color for widget backgrounds. highlight, HIGHLIGHT * Grey50 is the default for widget highlights. selected, SELECTED * Yellow is the default selected color for widgets. datazone, DATAZONE * Black is the default datazone color for widgets. PM Unselected Color, PRESENTATION_UNSEL_COLOR The color that is used for presentation templates for all regions that are not the selected region. The default is {130,170,255} which is a light blue. Data Color: Slot n Real, DATA_COLORS_n.REAL * Data Color: Slot n Imaginary, DATA_COLORS_n.IMAG * Where n is a letter from A through G. These control the color of the display data in different slots in a geometry. A through F represent slots 1 through 6, where A is the color of the data in the rst slot and every 6th slot thereafter; B is the color in the second slot and every sixth slot thereafter, etc. Color G is a grey scale color used if Delta is in Black & White mode. Peak Color n, PEAK_COLORS_n * n is a letter from A through P. These are the colors of the sequence markers for peak pick labels. They can be changed using the spreadsheet tool, where A through
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P represent Colors 0-16 on the spreadsheet. The default for each preference is white. Molecule Bond Color n, MOLECULE_BOND_COLOR_n n is a number 1 to 10. These are the colors in which the molecule bonds will be drawn for molecule window n. The default for each preference is white. System Page Address Book, ADDRESS_BOOK_FILE If this le is specied, then this le will be used for the address book in the Send Mail Percival program. Allow Author Login, ALLOW_AUTHOR_LOGIN ON/OFF. When ON, the Master Console wont come up immediately when Delta starts, instead, a pop-up box lets you select your logon name from a list. When you exit Delta, the popup box has an additional box that allows you to change your name, log off and log on as a different user. The default is OFF. Auto Directory Submit, AUTO_DIRECTORY_SUBMIT * ON/OFF. When ON, any experiment le that is placed in the spectrometer directories under /usr/tmp/ will automatically be submitted to the spectrometer. The default is OFF. Bell Sound, BELL A lename specifying the sounds (.aiff) le to play when the Bell function is called. There is not default for this parameter. Black and White Icons, ICONS_BW ON/OFF. When ON, Delta will display all pushbutton icons in black and white. The default is OFF. Color Mode, DEPTH_8BIT * DITHER/COLOR_INDEX/EXTENDED_COLOR. The color mode in which Delta will run. This preference applies only to 8 Bit color systems and is ignored on 24 Bit color systems. The default is DITHER. Console Log File, CONSOLE_LOG_FILE If this preference is clear, then logging console lines is off. However, if it is a filename then all Delta Console output is saved in this file. If the filename does not include a path, then the Report Output path is assumed. FID Audio, FID_AUDIO ON/OFF. The Vector View tool has the ability to show a FID while the experiment is being collected. When ON, the FID will be played through the system's audio hardware. The default is OFF.
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Operator Cache, OPERATOR_CACHE * ON/OFF. When ON, Percival operators are cached when loaded. When OFF, every time an operator is referenced, it must be loaded from disk. The default is ON. Single Buffering, BUFFERING * ON/OFF. When this value is not any of the values 1, single, or OFF, Delta will run with Double Buffering Mode turned on. The default is OFF. Spectrometer Monitor, SPECTROMETER.CONTROL.MONITOR ON/OFF. When ON, and the Spectrometer Tool is connected to a spectrometer, a sampling of the spectrometer's current values is displayed on the bottom of the tool. When OFF, this info is hidden.The default is OFF. Spectrometer Load/Eject Disable, SPECTROMETER.LOAD_EJECT_DISABLE ON/OFF. When ON, and the spectrometer has an auto sample changer connected to it, the Load and Eject buttons will be disabled on the Sample Tool. The default is OFF. Miscellaneous Page Acquisition Auto-Place, ACQ_AUTO_PLACEMENT ON/OFF. When ON, then when a data le comes back from collection, the appropriate data processing tool will appear automatically on the screen. If OFF then only a red outline will appear and the user must place the tool. Set to ON if you will be collecting many data sets and will be away from the workstation. The default is OFF. Auto Level Tool, LEVEL_TOOL_ON ON/OFF. When ON and the rst geometry is appears on the desktop, a Level Tool will automatically appear. The default is OFF. Auto Console, MASTER_CONSOLE.CONSOLE * ON/OFF. When ON, the console input box is displayed on the bottom of the Delta Console when Delta starts. The default is ON. Console Coloring, CONSOLE_COLORING ON/OFF. When ON, certain types of output to the Delta Console will be color coded. The default is OFF. Console Color, MASTER_CONSOLE.CONSOLE_COLOR * The color for the Delta Console input box. The default is yellow. Console Cut & Paste, MASTER_CONSOLE.CUT_PASTE_TOOLS * ON/OFF. When ON, the cut and paste tools on the Master Console will be
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available. The default is ON. Console History, MASTER_CONSOLE.MAX_LINES * The number of lines in the console that are kept in memory. The default is 512. Console Wrap, MASTER_CONSOLE.TEXT_WRAP * ON/OFF. When ON, long messages that are sent to the console screen will wrap to the next line. Cosy Peak J Width, COSY_PEAK_J_WIDTH The J-Coupling width (in Hertz or PPM) used for auto peak picking. Peaks within this width are considered a single peak and will not be picked more than once. Setting this preference to 0 will disable this feature. The default is 0[Hz]. Geom Tools: Save State, GEOMETRY_TOOLS.SAVE_STATE ON/OFF. When ON, the current opened state of the Level Tool is saved in the preference le. Also when the level tool is displayed or hidden, the level_tool_on preference is updated. The default is OFF. Geom Tools: Tracking, GEOMETRY_TOOLS.TRACKING ON/OFF. When ON, the Level Tools position is stored so that when it is restarted, it will reappear at the same location as when it was closed. Integral Search Width, INTEGRAL_SEARCH_WIDTH The minimum distance (in Hertz or PPM) two peaks must be separated in order to have separate integrals created for them. The default is 25[Hz]. Level Tool: Auto Apply, LEVEL_TOOL.AUTO_APPLY ON/OFF. When ON, and Contour Line Check is also ON, changes made with the Level Tool will effect the display of the data immediately. The default is OFF. Level Tool: Pop, LEVEL_TOOL.AUTO_POP ON/OFF. When ON, then when the space bar is pressed with the Level Tool open, the Level Tool will be popped to the front. The default is OFF. Preserve Position, DELTA_TOOLS.PRESERVE_STATE ON/OFF. When ON, the size and locations of most Delta tools will remember their size and location on the desktop between Delta sessions. A .tool_name.XY_POS conguration entry will be placed in the conguration le to store the tools current size and position. This will also cause a these tools to be automatically placed on the screen when they are opened. The default is OFF. Save Color & Font, SAVE_COLOR_FONT ON/OFF. When ON, any colors and fonts that were changed and saved with the Widget Editor will be remembered each time the tool is opened. Otherwise, any modied features are ignored. The default is OFF.
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Show Deconvolution Results, SHOW_DECONVOLUTION_RESULTS ON/OFF. When ON, then when data is deconvolved, the results of the deconvolution will display in the Delta Console. The default is ON. Show Peak Count, SHOW_PEAK_COUNT ON/OFF. When ON, then when data is automatically peak-picked, the number of peaks found will display in the Delta Console. The default is OFF. Sweep/Offset Adjust, AUTOMATIC_SWEEP_OFFSET ON/OFF. When ON, and a change is made in the Experiment Tool to an experiments domain parameter on any axis, the experiment automatically updates its corresponding sweep width and offset. The default is ON. Date Format String, DATE_FORMAT A call to the get_date_format operator will return the date/time formatted according to this value. The following special characters (shown below in bold) will be replaced with the appropriate information. The default is %M %d, %y. %m will be replaced by the 3 letter month abbreviation. %M will be replaced by the full Month name. %n will be replaced by the Month number. %d will be replaced by the day number. %w will be replaced by the 3 letter weekday abbreviation. %W will be replaced by the full weekday name. %y will be replaced by the year number. %t will be replaced by the time. (hh - mm - ss) Tools Page The Delta Tools page contains user-congurable tool parameter toggles. Automation Console window, otherwise the user will only be allowed to monitor the spectrometer. The default is OFF. Allow Connect, AUTO_CONSOLE.CONNECT When TRUE, the user is allowed to connect to a spectrometer in the Automation Console window; otherwise a user may only monitor a spectrometer. Connect Tool Init, CONNECT_TOOL.AUTO_INITIALIZE ON/OFF. When ON, and the user pushes the Connect button on the Connect Tool, the tool will re-initializes itself to {None, None, None} indicating that the X, Y, and Z axis are ready for a new connection to be set. The default is OFF. Convert: Auto Extension, CONVERT.AUTOEXTENSION ON/FALE. When ON, automatically x up the resulting data le extension. The default is ON.
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Convert: Quiet, CONVERT.QUIET ON/OFF. When ON, progress messages will not be displayed in the status area of the Convert Tool. The default is OFF. Data Slate: Connect X, DATA_SLATE.CONNECT.X ON/OFF. When ON, current zoom coordinates will be propagated to other geometries in the same Data Slate in the X dimension only. The default is OFF. Data Slate: Connect All, DATA_SLATE.CONNECT.ALL ON/OFF. When ON, current zoom coordinates will be propagated to all other geometries in every dimension.
Note: Connect X and Connect All cannot both be ON. If this is the case, then Connect All has precedence. Data Slate: Connect Features, DATA_SLATE.CONNECT.FEATURES ON/OFF. When ON, and a geometry feature is modied, that change is propagated to all other geometries in that Data Slate. When OFF, features remain specic to individual les. The default is ON. Data Slate: Plot Parameters, DATA_SLATE.PLOT_PARAMS ON/OFF. When ON, and a le is printed from Data Slate, the les parameters are printed with the data. The default is OFF. Data Slate: Plot Process List, DATA_SLATE.PLOT_PROCESS_LIST ON/OFF. When ON, and a le is printed from Data Slate, any processing list that was stored in the le will be plotted with the data. The default is OFF. Data Slate: Save Plot Parameters, DATA_SLATE.SAVE_PLOT_PARAMS ON/OFF. When ON, the current state of Data Slate: Plot Parameters is stored when its state is changed. The default is OFF. Data Slate: View Orientation, DATA_SLATE.VIEW_ORIENTATION HORIZONTAL/VERTICAL/BOX. Sets the default geometry organization for Data Slate. The default is HORIZONTAL. Experiment Tool: Hints, EXPERIMENT_TOOL.HINTS ON/OFF. When ON, the labels in the Experiment Tool will look like buttons to indicate to the user that clicking on the labels allow the user to modify parameter values. When OFF, the button look is missing, but the user can still click on the label to modify the parameter. The default is ON. File Manager: Delete Whole Dir, FILE_MANAGER.DEL_WHOLE_DIR ON/OFF. When ON, and you delete a directory, the File Manager will recursively delete all les and other directories in the current directory. When OFF, you will
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only be able to delete a directory when it is empty. The default is OFF. File Manager: Delete Dir Update, FILE_MANAGER.SAVE_DEL_WHOLE_DIR ON/OFF. When ON, the current state of the File Manager: Delete Whole Dir preference is preserved between Delta sessions. The default is ON. File Manager: Purge Proc. Query FILE_MANAGER.PURGE_QUERY When ON, it pops up a dialog box when the purge processed button is pressed in the le manager. The dialog box prompts the user to press one of the following buttons; purge selected le only, purge all les in current directory, purge all les in current directory and in all sub-directories. The default is OFF. File Manager: Require Acknowledge, FILE_MANAGER.REQUIRE_ACK ON/OFF. When ON, and a potentially hazardous operation isrequested, the File Manager will display an Are you sure? message. The default is ON. File Manager: Require Ack Update, FILE_MANAGER.SAVE_REQUIRE_ACK ON/OFF. When ON, the current state of the File Manager: Require Acknowledge preference is preserved between Delta sessions. The default is ON. File Manager: Show Errors, FILE_MANAGER.COMPILE_ERROR ON/OFF. When ON, and compilation from the File Manager results in errors and/ or warnings, then a box is displayed with the compilation results. When OFF, the user is only informed of compilation status by an acknowledge box. The default is ON. File Manager; Show Errors Update, FILE_MANAGER.SAVE_COMPILE_ERROR When ON, the current state of the Show Errors preference is saved between Delta sessions. File Manager: Show Hidden Files, FILE_MANAGER.SHOW_HIDDEN ON/OFF. When ON, hidden les (those whose lename begins with a . in UNIX) are displayed in the directory list box. When OFF, all hidden les and directories are not included in the le list. The default is OFF.File Manager: Show Errors Update, FILE_MANAGER.SAVE_COMPILE_ERROR ON/OFF. When ON, the current state of the File Manager: Show Errors preference is preserved between Delta sessions. The default is ON. File Manager: Version Keep, FILE_MANAGER.KEEP Species the number of les to keep when the Delete All button is pressed in the File Manager. Version 1 is always kept and counts toward the number to keep. The default is 2. PM: Center Y-Scale, PRESENTATION.CENTER_Y_SCALE ON/OFF. When ON, the geometry plotted with the Presentation Manager will be centered around 0 and then the data will be Y-scaled to the top of the geometry.
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When OFF, the data will be maximized to the extents of the geometry and then Yscaled. The default is ON. PM: Font Size, PRESENTATION.FONT_SIZE The font size to use for plotting data from the Presentation Manager. The default is 10.6. PM: Plot Process List, PRESENTATION.PLOT_PROCESS_LIST ON/OFF. When ON, and a box in a Presentation Manager template is set up to print the acquisition parameters of a le, then the processing list for that data le will also be printed. When OFF, only the acquisition parameters will be printed. The default is OFF. Preferences: Start Page, PREFERENCES.START_PAGE The name or number of the Preferences page that will be displayed when the Preferences Tool is started (e.g., personal). Sample Tool: Gradient Shim Allowed, SAMPLE_TOOL.GRADIENT_SHIM_ALLOWED ON/OFF. When ON, the Gradient Shimming buttons will be functional from the Sample Tool. The default is OFF. Sample Tool: Verify, SAMPLE_TOOL.VERIFY ON/OFF. When ON, if the user attempts to change the system shims, a pop-up box is displayed to make sure the user really intends to do this. The default is ON. Spectrometer Tool: Double-Click, SPEC_TOOL.DOUBLE_CLICK_ACTION CONNECT/MONITOR. When the user double-clicks on a spectrometer link in the Spectrometer Tool, you will automatically link to the spectrometer in Connect or Monitor mode respectively. The default is CONNECT. Vector View: Auto Off, VECTOR_VIEW.AUTO_OFF ON/OFF. When ON, the Vector View tool automatically shuts off the data display after 4 minutes. When OFF, the data display is shut off after 30 minutes. The default is ON. Vector View: Processing, VECTOR_VIEW.PROCESSING A set of possible processing options to perform prior to display in the Vector View tool. The possible strings that may be included in this set are: DC_BALANCE, WINDOW, FFT, PHASE, DC_CORRECT, ABS, and AUTOPHASE.
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Processors Page Data Processors: These parameters are used for the Data Processors only: Process 1D: Auto Apply, PROCESS_ONED.AUTO_APPLY ON/OFF. When ON, the Auto Apply button will be on (depressed) when 1D Processor starts. This will cause changes to the processing list to be carried out immediately. The default is OFF. Process 1D: Show FID, PROCESS_ONED.FID ON/OFF. When ON, the original data window is displayed above the processed data window in 1D Processor. The default is ON. Process 1D: Show Macros, PROCESS_ONED.MACRO_BUTTONS ON/OFF. When ON, the row of processing macro buttons is displayed below the tool bar in 1D Processor. The default is ON. Process 1D: Macro Denition, PROCESS_ONED.MACRO_DEF The set of operations to perform for each of the 1D Processor macro buttons. Do not attempt to edit this preference directly. Use the editor provided by Process 1D. Process 1D: Macro Order, PROCESS_ONED.MACRO_PAD_ORDER Indicates the order in which the macro buttons appear in 1D Processor. Process 1D: View Precision, PROCESS_ONED.VIEW_PRECISION The number of decimal places displayed in the view control tool of 1D Processor. The default is 2. Process 1D: Phase Step P0 PROCESS_ONED.PHASE_STEP.P1 Default is 1. Number which indicates the step size of the phase box in the 1D processor. Process 1D: Phase Step P1 PROCESS_ONED.PHASE_STEP.P0 Default is 0.25. Number which indicates the step size of the phase box in the 1D processor. Process 1D: Plot Parameters, PROCESS_ONED.PLOT_PARAMS ON/OFF. When ON, then when data is printed from 1D Processor, the data's acquisition parameters are printed with the data. The default is OFF. Process 1D: Plot Process List, PROCESS_ONED.PLOT_PROCESS_LIST ON/OFF. When ON, then when data is printed from 1D Processor, the processing list (if available) is printed with the data. The default is OFF. Process 1D: Save Auto Apply, PROCESS_ONED.SAVE_AUTO_APPLY
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ON/OFF. When ON, then the state of the Auto Apply button is preserved between 1D Processor sessions. The default is OFF. Process 1D: Save FID, PROCESS_ONED.SAVE_FID ON/OFF. When ON, then the visibility state of the original data window will be preserved between 1D Processor sessions. The default is OFF. Process 1D: Save Macro Def., PROCESS_ONED.SAVE_MACDEF ON/OFF. When ON, then the macro denitions are saved when they are modied so the new denitions will be available in future 1D Processor sessions. The default is OFF. Process 1D: Save Macros, PROCESS_ONED.SAVE_MACRO ON/OFF. When ON, then the visibility state of the macro pad will be preserved between 1D Processor sessions. The default is OFF. Process 1D: Save Plot Param, PROCESS_ONED.SAVE_PARAM ON/OFF. When ON, then the state of whether or not to print data parameters (indicated by the Process 1D: Plot Parameters preference) is preserved between 1D Processor sessions. The default is OFF. Process 1D: Save Simple Mode, PROCESS_ONED.SAVE_SIMPLE ON/OFF. When ON, then the Process 1D: Simple Mode state is saved each time that it is changed so that the state is preserved between 1D Processor sessions. The default is OFF. Process 1D: Save Timing, PROCESS_ONED.SAVE_TIMING ON/OFF. When ON, then the Process 1D: Show Timing state is saved each time that it is changed so that the state is preserved between 1D Processor sessions. The default is OFF. Process 1D: Save Tools, PROCESS_ONED.SAVE_TOOLS ON/OFF. When ON, then the visibility state of the processing tools is preserved between 1D Processor sessions. The default is OFF. Process 1D: Simple Mode, PROCESS_ONED.SIMPLE_MODE ON/OFF. When ON, then 1D Processor will start in Simple Mode. Otherwise, the processing list features are enabled to provide exible processing control. The default is OFF. Process 1D: Show Timing, PROCESS_ONED.TIMING ON/OFF. When ON, the total processing time is displayed on the Delta Console each time the le is processed in 1D Processor. The default is OFF. Process 1D: Show Tools, PROCESS_ONED.TOOLS ON/OFF. When ON, the processing tools in 1D Processor (macro buttons, processing list, and phasing control) will be visible and available to use. The
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default is ON. Process nD: Plot Parameters, PROCESS_ND.PLOT_PARAMS ON/OFF. When ON, then the acquisition parameters will be printed with the data when printing from nD Processor. The default is OFF. Process nD: Plot Process List, PROCESS_ND.PLOT_PROCESS_LIST ON/OFF. When ON, then the processing list will be printed with the data when printing from nD Processor. The default is OFF. Automation Page Advanced Automation, AUTOMATION.ADVANCED ON/OFF. When ON, the Automation Tool comes up with Advanced Mode set on allowing the user to modify some of the experiment parameters before the automation is submitted. The default is OFF. Advanced Automation Lock, AUTOMATION.ADVANCED.LOCK ON/OFF. When ON, and Advanced Automation is set to OFF, the user will not be allowed to enter Advanced Mode. The default is OFF. Advanced Automation Sample, AUTOMATION.ADVANCED.SAMPLE ON/OFF. When ON, the filename and sample ID will be considered separate and the user will be able to specify each individually. Otherwise, the filename box will set both the filename and the Sample ID. The default is OFF. Allow Export Email, AUTOMATION.ALLOW_EXPORT_EMAIL When ON, a second email address box is shown on the automation window to allow you to specify email address(es) to which to send the collected data sets. When this box is not displayed, it is not possible the send the data via email. It defaults to OFF. Allow Initialize, AUTOMATION.ALLOW_INITIALIZE ON/OFF. When ON, and the Automation Tool is in Advanced Mode, the user will be able to add and modify job parameters. The default is ON. Append Date, AUTOMATION.DATE_FILENAME ON/OFF. When ON, data files returned from automation will have the date (specified by the Date Format String preference) appended to the resulting filename. The default is OFF. Conrmation, AUTOMATION_CONFIRMATION ON/OFF. When ON, a dialog box will appear when a method is submitted from the Automation Tool requesting conrmation of some parameters. The dialog box will time-out in 15 seconds if a response is not given and continue to run the submitted method. The default is ON.
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Email File, AUTOMATION_EMAIL_FILE If this preference is specied with a complete path, the indicated le will be mailed to inform users that an automation job is completed. If this is not specied, then a default message will be sent. There is no default for this parameter. EMail Hold, AUTOMATION_EMAIL_HOLD ON/OFF. When ON, the e-mail line will not be cleared when the Filename or the Slot lines in the Automation Tool are changed. The default is OFF. Email Limitation, AUTOMATION.EMAIL_LIMITATION ON/OFF. When ON, the user submitting automation templates to run will only be able to select E-mail notication to predened people. When OFF, the user may enter any E-mail address. Defaults to OFF. Gradient Shim, AUTOMATION.GRADIENT_SHIM ON/OFF. If ON, then when a method is submitted to the spectrometer, gradient shimming will be executed before the rst experiment and also before subsequent experiments if the lock state is found to be off or the slot has been changed. The default is OFF. Gradient Shim Allowed, AUTOMATION.GRADIENT_SHIM_ALLOWED ON/OFF. When ON, then Gradient Shimming will available in the Automation menu. See Automation: Gradient Shim. The default is OFF. Hours, AUTOMATION.HOURS ON/OFF. When ON, the automation.hours.machine_ident le will be checked when an Automation method is submitted to the queue. If the expected runtime of the entire Method is longer than the allowed time, then the method will be delayed. The default is OFF. Set Init_Group on Failure, AUTOMATION.INIT_GROUP_ON_FAILURE, When gradient shimming cannot run from Automation, the INIT_GROUP experiment parameter will be set to this value. If gradient shimming succeeds, then the INIT_GROUP parameter will not be modied. Show Times, AUTOMATION.SHOW_TIME When ON, a dialogue box will appear when a method is submitted from Automation showing the estimated time to complete the method. The dialog box will automatically choose Continue in 30 seconds if the user does not select a button rst. Supervisor Alert, SUPERVISOR_ALERT This is the E-mail address of the person who will receive E-mail when a group of experiments in Automation does not complete successfully.There is no default for this parameter.
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Supervisor Email Always, SUPERVISOR_EMAIL_ALWAYS When ON, E-mail will be sent to the supervisor (specied by Supervisor Alert) showing the list of experiments that were run when the Method is complete. Temperature Lock, AUTOMATION.TEMPERATURE.LOCK ON/OFF. When ON, the user will not be allowed to modify the temperature values set in the automation template. The default is OFF. Tubeless NMR, AUTOMATION.TUBELESS ON/OFF. When ON, the Automation Tool will be enhanced to support liquid (tubeless) NMR. The default is OFF.
PARAMETER CONTROL FILES

delta_parameters.master_list This le contains a list of common acquisition parameters. This le resides in the users template directory. The template directory is specied in the .delta_configure le. delta_parameters.default delta_parameters.1D delta_parameters.2D delta_parameters.3D These les contain acquisition parameters, tailored for general, 1, 2, and 3 dimensional les, that you would like to appear on plots where the acquisition parameters are requested to be displayed. They are created from the delta_parameters.master_list le using the Delta Parameter Editor. If the le(s) are not present then a short list of equation parameters is displayed on the plot. These les reside in the user's template directory. The template directory is specied in the .delta_configure le.
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USER MENU DEFINITION FILE

.delta_user This le is used to create a custom menu of commands for the Delta Console and the Automation Console. This additional menu is titled User. The basic layout of the le .delta_user is: menu-choice | command where each of the above statements is on a single line. menu-choice is either a single title designating a menu choice in the User menu, or a series of sub-menu titles, separated by > signs, to create a menu choice in a sub-menu of the User menu. command is a Percival code element which executes a new program or an operator. For example: a) to add File Manager to the User menu, use the following line: File Manager | new file_manager b) to create an entry Tic-Tac-Toe in a Games sub-menu in the User menu the following line could be used: Games>Tic-Tac-Toe | spawn eval tic_tac_toe In the above examples, the command new is used to execute a Percival program, and spawn eval is used to execute a Percival operator.
Note: These entries are case sensitive, so type them as you want them to appear in the menu.
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ECLIPSE SPECTROMETER FILES AND DIRECTORIES

This section is only applicable to Eclipse and Delta-Upgrade systems that can control a spectrometer. Root Directory This is the superuser account for the Eclipse system, and normally the only active account on the acquisition system. The initial login directory for this account is the / directory. /eclipse/ Conguration Files gamma.def This le contains the gyromagnetic ratios for a large number of nuclei. machine.cong This le is the primary conguration le for the Eclipse+ NMR spectrometer. Sample machine.cong le for an Eclipse+ 300 NMR spectrometer:
----- Machine specific configuration information --- Possible Instrument Types : ECLIPSE+, ECLIPSE, GSX, or PHANTOM INST_TYPE = ECLIPSE+ -- Spectrometer Configuration FIELD = 7.0586013 tesla PULSER_TICK = 100.0 --ADC = 16/200kHz/60 ADC = 16/1MHz/20 -- Oscillator Configuration Table. Channels : obs1 obs2 irr1 irr2 tri qua -- ( Specify Fixed-Oscillator Nuclei as 1H 3H 13C 15N 19F 31P etc. ) obs1 = 1H 13C -- HPRC obs2 = NONE irr1 = 1H 13C -- HPRC irr2 = NONE tri = NONE qua = NONE -- Fixed-Oscillator Frequencies OSC_1H = 300.40 MHz OSC_3H = 320.40 MHz OSC_13C = 75.45 MHz OSC_15N = 30.35 MHz OSC_19F = 282.65 MHz OSC_31P = 121.50 MHz -- Field Gradient Controller Type ( NONE, SINGLE_SHAPE, MULTI_SHAPE ) GRADIENT = NONE
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Eclipse Spectrometer Files and Directories
-- Field Gradient Axis FG_CONTROLLABLE_X_AXIS FG_CONTROLLABLE_Y_AXIS FG_CONTROLLABLE_Z_AXIS
Controllability Settings = FALSE = FALSE = FALSE
-- RF Shaper present/not present for OBS/IRR and TRI/QUA channels RF_SHAPER_AVAILABLE_OBS_IRR = FALSE RF_SHAPER_AVAILABLE_TRI_QUA = FALSE -- Lagrange Shim System present/not present LG_SHIMS = FALSE --SAWTOOTH_SHIFT = 7 --SAWTOOTH_TRIM = 1.17 -- Auto-Gain Parameters AUTOGAIN_UPPER = 85.0 AUTOGAIN_LOWER = 60.0 -- Digital Filter Parameters FILTER_LIMIT = 8 MAX_FILTER_POINTS = 65536 -- Number of slots in changer or zero if no changer is present OPERATION_PROTECT = TRUE CHANGER = 0 CHANGER_VERSION = 1 CHANGER_TIMEOUT = 45 SPIN_SLOP = 3.0 -- Source of gas for sample spin operation ( AIR, N2 ) SPIN_GAS_SOURCE = AIR -- low and high temp range of VT unit or 0 0 if no unit is present VTEMP = -150 180 --TEMP_SLOP = 3.0 -- Maximum duration in seconds of VT TEMP_HOLD state while sample ejected. TEMP_HOLD_TIMEOUT = 30 -- Low cryogen alarm levels in percent LOW_N2 = 10.0 LOW_HE = 25.0 -- Retry and expire times for the file upload manager UPLOAD_RETRY = 15.0 -- minutes UPLOAD_EXPIRE = 10080.0 -- minutes, default 7 days -- Queue Management ALLOW_OWNED = ALLOW_MONITOR = IDLE_LOCK = Parameters TRUE FALSE FALSE
-- Queue Delay information in seconds SAMPLE_DELAY = 600.0 PROBE_DELAY = 30.0 HOLD_DELAY = 600.0 -- Log file turn over control. -- List days of week, separated with spaces, to turn over log -- SUN MON TUE WED THR FRI SAT
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MACHINE_LOG QUEUE_LOG
= TUE FRI = FRI
--Sound files READY_SOUND = /eclipse/ready.aifc SAMPLE_SOUND = /eclipse/sample.aifc PROBE_SOUND = /eclipse/probe.aifc COLLECTED_SOUND = /eclipse/collected.aifc NOT_COLLECTED_SOUND = /eclipse/not_collected.aifc -- CPF/GSX/GX Specific --GSX_AUTOLOCK_TRANS = --SAWTOOTH_SHIFT = --SAWTOOTH_TRIM = parameters 255 9 1.22
-- AQP3 ADC pipeline depth ADC_PIPELINE_DEPTH = 1 -- Strictly Enforce Solvent Temperature Limits during experiments. STRICT_SOLVENT_TEMP_LIMITS = FALSE -- Shim knob box present SHIM_KNOB_BOX = FALSE -- Shim knob box Load/Eject, Spin, Lock buttons disabled on EX instruments SHIM_KNOB_BOX_LOCKOUT = TRUE -- Operate B-bus devices in CONNECT mode. CONNECT_DEVICES = TRUE
Standard machine.cong le entries Below is a complete list of the spectrometer conguration parameters. Many of these are used to enable specic accessories or special features available only to spectrometers equipped with certain hardware systems. Use any conguration parameters not appearing in the distributed machine.config le with caution. ADC Denes the resolution and speed of the installed Analog-to-Digital Converters. The entries are in pairs. The rst number is the digital range of the ADC in bits. The second number is the maximum speed of the ADC in Hertz. If more than one ADC is in the acquisition system they can be appended to this entry separated by a space. ADC_PIPELINE_DEPTH Species which type of ADC board is being used in the Acquisition System. For ADC boards with two BNC Twin-Ax connectors: ADC_PIPELINE_DEPTH = 1. For ADC board with two JST 3-pin connectors: ADC_PIPELINE_DEPTH = 3. The default is 3. ALLOW_MONITOR This eld indicates whether more than one Delta workstation can connect to the
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instrument and get back real-time views of the data as it is acquired. The default is FALSE. ALLOW_OWNED When this ag is TRUE, it allows the Eclipse spectrometer to operate in Connect or Console (single user) Mode. It is then said that the user owns the spectrometer. When this ag is FALSE, the user may only enter Monitor Mode on the spectrometer, and only users with console privilege can own the spectrometer. Owning the spectrometer allows the user to run interactive experiments such as sawtooth. If the user does not own the spectrometer, experiments may only be submitted to the experiment queue. The default is TRUE. AQP3_VERSION Species the AQP3 board version: (0 or 1). The default is 0. AUTOGAIN_LOWER AUTOGAIN_UPPER These entries dene the lower and upper limits, in percent, for the Free Induction Decay signal intensity when using the automatic gain-setting feature. For AUTOGAIN_LOWER, the default is 60.0. For AUTOGAIN_UPPER, the default is 85.0. BBUS_INTERFACE_BOARD Species whether or not the instrument is equipped with a B-Bus Interface Board. The default is FALSE. CHANGER Denes the number of samples that the installed Auto-Sample Changer can hold at one time. Systems without an Auto-Sample Changer have a value of 0. Currently JEOL supplies 3, 8, 16, and 64 sample changers. The default is 0. CHANGER_MAX_CHANGE_TIME Species the maximum time, in seconds, allowed for completion of an AutoSample Changer load or store operation before a time-out condition can be recognized and acted upon. The default is 45 seconds. CHANGER_TIMEOUT Species the maximum time, in seconds, allowed for completion of an AutoSample Changer load operation before an experiment that requires the specied sample slot is moved down in the experiment queue to be attempted later. The default is 300 seconds. CHANGER_VERSION Denes the Auto Sample Changer software ROM version: 0 = pre-Eclipse+ and 1 = Eclipse+ The default is 0.
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COLLECTED_SOUND The location of the sound le used to inform the user that an experiment has completed successfully. CONNECT_DEVICES Species whether instrument B-Bus hardware devices are to be operated in connected or disconnected mode. This setting affects the alarm presentation behavior of B-Bus devices. The default is FALSE. FG_CONTROLLABLE_X_AXIS FG_CONTROLLABLE_Y_AXIS FG_CONTROLLABLE_Z_AXIS Species whether eld gradient control is available on the X, Y and Z axes, respectively. Default to FALSE. FIELD Denes the magnetic eld strength, in Tesla, for the Eclipse spectrometer. This value is used with the gamma.def le to calculate the actual observation frequencies of the desired nucleus. FILTER_LIMIT Species the maximum number of times that the data can be over-sampled when digital ltering is turned on. The default is 8. GRADIENT Species eld gradient controller MULTI_SHAPE). The default is NONE.
type:
(NONE,
SINGLE_SHAPE,
GSX_AUTOLOCK_TRANS Species the threshold at which the autolock value in the solvent.def le is changed to 0 or 1 for the GSX/GX/CPF lock modules. The default is 0. GSX_COMPAT Denes whether this instrument is compatible with instrument control as dened for a GSX spectrometer. The default is FALSE. HOLD_DELAY Denes how long the Eclipse acquisition system will wait for the host to complete data processing and submit a new experiment with parameters determined from the most recent experiment. The default is 600.0. IDLE_LOCK Controls whether the machine.idle_lock le is executed when there are no experiments in the queue and no one owns the spectrometer. The default is FALSE.
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IDLE_LOCK_DELAY Species the delay, in seconds, after the conditions for execution of the machine.idle_lock le exist, to wait before entering the idle_lock state. Default to 120.0. INST_TYPE Denes the machine type. Supported machine types are Eclipse+, Eclipse, GSX, and Phantom. The GSX instrument type is used for JEOL GX, GSX, and CPF NMR spectrometers. The Phantom instrument type is used to demonstrate experiment control when a spectrometer is not available. The default is ECLIPSE. LG_SHIMS Species whether there is a Lagrange Shim system connected to the spectrometer. The default is FALSE. LOCK_TIMEOUT The length of time in seconds that the sample queue will wait for the lock to indicate lock on. The default is 300.0. LOW_HE Denes the level, in percent, at which the helium warning light on the front of the Eclipse acquisition system will come on. The default is 10.0. LOW_N2 Denes the level, in percent, at which the nitrogen warning light on the front of the Eclipse acquisition system will come on. The default is 10.0. MACHINE_LOG This entry denes the days of the week that the machine.log le is turned over to the machine.old le for Sunday through Saturday. The default is (FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE) MAGNET_DRIFT_RATE_HZ_PER_HR Species the magnetic eld drift rate in Hz per hour. A value of 0.0 causes the automatic magnetic-eld drift-correction function to be inactive. When a load system shim call is issued, the software calculates the time difference between current time and the last time the system shims were save and corrects the Z0 shim automatically. This action is not carried out if the value = 0.0. Note: It is important that the spectrometer be still shimmed on a regular basis and the system shims saved to disk. The default value is 0.0. MAX_FG_PULSE Species the maximum duration, in seconds, that the multi-shape eld gradient amplier can safely drive its outputs at 100% power. The default is 100.0E-3. (1/10 second).
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MAX_FILTER_POINTS Species the maximum number of points that can be digitally ltered. FILTER_FACTOR * X_POINTS cannot be larger than MAX_FILTER_POINTS. The default is 64 * 1024. MAX_POINTS Denes the maximum number of data points collected in a single experiment. For an AQP3, the default is 1024 * 1024. For other units, the default is 512 * 1024. MAX_PULSE_SEQUENCE_BYTES Denes the maximum size, in bytes, of the compiled pulse sequence for download to the pulsar. The default is 8192. MAX_SCANS Denes the maximum number of experiment scans allowable in an experiment. The default is 2**15 - 1. MINIMUM_LOCK_STRENGTH Denes the minimum value of lock-signal strength sufcient to insure that the lock oscillator is functioning. The default is 50.0. NOT_COLLECTED_SOUND The location of the sound le used to inform the user that the experiment was not collected successfully. OBS1, OBS2, IRR1, IRR2, TRI, QUA These entries dene what type of oscillator is available to each RF channel. The values for each RF channel are specied as the atomic number followed by the periodic table element symbol. To specify a High Precision Offset for any channel, remove the -- before the HPRC designator. This will cause the channel to be treated like a High Precision Offset by the Control software. OPERATION_PROTECT Controls the multitasking abilities of an Eclipse NMR spectrometer. When set to TRUE, only one operation at a time is allowed on the spectrometer. The default is TRUE. OSC_1H, OSC_3H, OSC_13C, OSC_15N, OSC_19F, OSC_31P These entries dene the xed oscillator frequencies for those nuclei for which xed oscillators are manufactured. The values shown below are typical for a 300 MHz spectrometer. OSC_1H = 300.40 MHz OSC_3H = 320.40 MHz OSC_13C = 75.45 MHz OSC_15N = 30.35 MHz
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OSC_19F = 282.65 MHz OSC_31P = 121.50 MHz PRESERVE_DIALS_FILE Species whether the xxxx.dials le for an autotune probe should be deleted upon instrument power-up. The default is FALSE. PROBE_DELAY Denes how long, in seconds, the Eclipse acquisition system will wait for the probe to be changed before shifting the waiting experiment down in the queue. A specic probe must be requested in the experiment for this feature to be active. The default is 30.0. PROBE_SOUND The location of the sound le used to prompt the user to check the probe tuning. PULSER_TICK Denes the minimum pulser tick in nanoseconds for the NMR spectrometer. The default is 100.0. QUEUE_LOG Denes the days of the week that the queue.log le is turned over to the queue.old le for Sunday through Saturday. The default is (FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE). READY_SOUND The location of the sound le used to inform the user that the spectrometer has nished its boot-up procedure. RF_SHAPER_AVAILABLE_OBS_IRR RF_SHAPER_AVAILABLE_TRI_QUA Specify whether an RF Shaper accessory is installed for use with the OBS and IRR channels, and for the TRI and QUA channels, respectively. Defaults are FALSE. SAMPLE_DELAY Denes how long, in seconds, the Eclipse acquisition system will wait for the sample to be changed before shifting the waiting experiment down in the queue. The default is 600.0. SAMPLE_SOUND The location of the sound le used to prompt the user to select a non-null sample id for a submitted experiment. SAWTOOTH_SHIFT This eld sets the reference point for sawtooth mode in the GX/GSX/CPF lock modules. The default is 6.
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SAWTOOTH_TRIM This eld adjusts the end points of the sawtooth range for the GX/GSX/CPF lock modules. The default is 1.0. SHIM_KNOB BOX Species whether there is a Shim Knob Box connected to the spectrometer. The default is FALSE. SOUND_DURATION The length of time in seconds that a sound event is repeated. The default is 45.0. SPIN_GAS_SOURCE Source of the pressurized gas for sample spin operation: (AIR or N2). The default is AIR. SPIN_SLOP Denes the slop, in Hertz, within which sample-spin setpoints are considered met to allow experiments to proceed. The default is 3.0. SPIN_TIMEOUT The length of time, in seconds, that the sample queue will wait for the sample spin speed to converge to within SPIN_SLOP of the desired spin speed setpoint before a fault may be recognized. The default is 120.0. STRICT_SOLVENT_TEMP_LIMITS Allows strict enforcement of solvent freezing and melting temperature limits, causing pop-up dialog boxes to display warning messages. Forces temperature limits violations to kill experiments when set to TRUE. The default is FALSE. SUPPRESS_FW_WARNINGS Species the version of instrument control software, in the format MAJOR.MINOR, which is expected to be run on the instrument. If a different version is run, checks if instrument rmware versions will be performed each time an experiment is started, and if dialog boxes that warn of older-than-latest versions will be displayed. The default is 0.0. SYNC0_BUS_LINE SYNC1_BUS_LINE SYNC2_BUS_LINE SYNC3_BUS_LINE Specify the instrument sync-bus masks for triggering the AQP3 units sync0 through sync3 lines. Defaults are 31. TEMP_HOLD_AVAILABLE Species whether the TEMP_HOLD variable temperature control feature is
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available. The default is TRUE. TEMP_HOLD_TIMEOUT Species the maximum duration, in seconds, that the TEMP_HOLD state can exist while the sample is ejected. The default is 120 seconds. TEMP_SLOP Denes the slop, in degrees Celsius, within which temperature setpoints are considered met to allow experiments to proceed. The default is 2.0. TEMP_TIMEOUT Denes the maximum time, in seconds, to wait for a temperature setpoint to converge to within TEMP_SLOP of the requested setpoint before posting a warning message. This time-out is in effect for experiments that do NOT use the SETTLE_VT header ag. The default is 600.0. TRIM_Z0_WHEN_LOCK_ON Species whether the automatic magnetic-eld drift-correction function is active during the LOCK ON state. For long term experiments, which are being acquired with the lock on, this correction can be included. Example: MAGNET_DRIFT_RATE_HZ_PER_HR = 6.4 Z0_HZ_PER_TICK = 2.0 TRIM_Z0_WHEN_LOCK_ON = TRUE When TRUE, drift correction can occur while LOCK is ON. When FALSE, drift correction cannot occur while LOCK is ON, but resumes when LOCK is OFF. The default value is FALSE. TSC_AVAILABLE Species whether a Tubeless Sample Changer is connected to the spectrometer. The default is FALSE. TSC_TIMEOUT Species the maximum time, in seconds, allowed for completion of a Tubeless Sample Changer load operation before the experiment is moved down in the experiment queue. The default is 300 seconds. UPLOAD_EXPIRE Denes the maximum amount of time, in seconds, that the Eclipse spectrometer will spend trying to upload a le when the user who submitted the experiment is not connected to the Eclipse spectrometer. The default is 6000.0. UPLOAD_RETRY Denes how often, in minutes, the Eclipse spectrometer will try to upload a le when the user who submitted the experiment is not connected to the Eclipse spectrometer. The default is 10.0.
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VTEMP Denes the absolute temperature extremes for operation of the variable temperature control system. These limits apply until superseded by any more stringent constraints found in a probe le. The default is 0 0. (This represents VT control unavailable). Z0_HZ_PER_TICK Species the change in Hz that result from a unit change in the value of the Z0 shim setting. For 300 and 400 MHz systems a single tick change of Z0 does not correspond to a 1[Hz] change. For these systems the relationship needs to be experimentally determined. We have determined that this value is roughly 2[Hz] per tick. Note: For 500 MHz and higher this value should be set to 1.0. The default value is 1.0. machine.lg_shims This le describes the names, ranges, increments, and units for the Lagrange shim system. machine.mx_shims This le describes the names, ranges, and increments for the matrix shim system. machine.info This le contains the spectrometer information text that is displayed when the info button is pressed on the spectrometer connection tool. A connection to a spectrometer is required before this information can be viewed. The '|' is used to indicate a new line in the display. Sample machine.info le: Eclipse 270 NMR Spectrometer| H/C Observation| H/C Irradiation| Variable Temperature Range: -150C to 180C machine.poll_speeds This le denes the standard polling rates in seconds for the instrument parameters listed in the le. These are the times between which measurements of the appropriate hardware are taken. Parameters not listed in this le are only polled on reference. Sample machine.poll_speeds le:
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LOCK_STRENGTH = 5 LOCK_PHASE = 60 LOCK_STATUS = 5 SPIN_GET = 5 TEMP_GET = 10 SAMPLE_STATUS = 5 SPIN_STATUS = 5 TEMP_STATUS = 5 N2_LEVEL = 600 HE_LEVEL = 600 AUTOSHIM_MODE = 20 SHIM_MAX_RECALL = 10 queue.hours This le controls the time limits for experiments submitted to the queue. The rst section denes the length of the ten time slots. The second section denes the usage of the time slots. An experiment submitted will be delayed until the calculated duration is shorter than the current slot time length. Times which are not specied are innite. This feature can be used to limit the length of experiments during prime-time hours. Sample queue.hours le: -- Time lengths in minutes. Non-specied times are innite. 1 180 2 300 3 480 4 3600 5 1440 6 7 8 9 0 -- Day/hour duration assignments. Non-specied blocks are innite. -- Note 24 hour time. hrs 012345678901234567890123 sun mon 333333311111111111222233 tue 333333311111111111222233 wed 333333311111111111222233 thr 333333311111111111222233 fri 333333311111111111444444 sat
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queue.priorities This le controls the priority of experiments that the user submits. This will allow projects or users to have experiments moved up or down the queue depending on the assigned priority. The user name in this le must match the user name in the user's .delta_configure le. The range of priorities is 0 to 255. Sample queue.priorities le: -- Queue priorities set by author name from the delta_congure le -- the default priority for names not in this table is 32 Mark = 33 Steve = 42 solvent.def This le denes the lock parameters for many standard solvents. Entries in this le include for each solvent: solvent name, solvent abbreviation, lock offset, lock level, lock gain, autolock level, melting point, and boiling point. The lock offsets in this le dene a chemical shift reference of 0.0 for a domain offset of 0.0 for protons. Other nuclei are also dened this way, but solvent effects will cause some deviation from zero for a standard reference compound. The melting and boiling temperatures for the solvent are used to warn the user when the VT system is set to a temperature that might freeze or boil the solvent.
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Machine action files
MACHINE ACTION FILES

These les are used to set default states of the instrument at different times during the normal operation of the Eclipse NMR Spectrometer. A complete list of possible parameters can be found in the Parameter tool located on the Spectrometer Control tool. machine.connect This le is run when the user connects to the Eclipse NMR Spectrometer. machine.defaults This le is executed before every experiment or job group of experiments. Sample machine.defaults le: -- Default parameter values loaded before experiment and upon connection RECVR_GAIN = 8.0 SPIN_SET = 15.0 SPIN_STATE = SPIN ON TEMP_STATE = TEMP OFF TEMP_SET = 26.0 LOCK_OSC_STATE = 2H OSC ON SAWTOOTH_RANGE = 4 machine.idle_lock This le is executed when the machine is idle and no one is connected to it. Normally this le is used to leave a standard sample in the magnet on instruments that have an Auto-Sample Changer. Sample machine.idle_lock le: CHANGER_SAMPLE = 1 SOLVENT = CHLOROFORM-D LOCK_STATE = AUTOLOCK machine.pre_exp This le is executed before a new job group of experiments is run on a particular sample. This le is run if: - the automatic ag is TRUE in the experiment header section, - the user owns the Eclipse NMR Spectrometer, - the pre_post ag is TRUE in the experiment header section. This le is also run if the user does not own the Eclipse NMR Spectrometer and the pre_post ag is TRUE in the experiment header section.
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machine.post_exp This le is executed after a job group of experiments is run on a particular sample. This le is run if: - the automatic ag is TRUE in the experiment header section. - the user owns the Eclipse NMR Spectrometer. - the pre_post ag is TRUE in the experiment header section. This le is also run if the user does not own the Eclipse NMR Spectrometer and the pre_post ag is TRUE in the experiment header section. /eclipse/probes/ This directory contains les that specify parameters for individual NMR probes. Each probe can have up to 4 les: xxxx.probe, xxxx.shims, xxxx.limits, and xxxx.dials. xxxx is the 4 digit probe number that is unique to each type of JEOL NMR probe. xxxx.probe This le describes the default spectroscopic and tuning parameters for a specic NMR probe. Sample xxxx.probe le: probe 5mm_Broadband 1412 Tunable Proton 1H Carbon 13C irr_code = 146 90 = 10.0 10.0 50.0 spin_lock_90 = 100 spin_lock_attn = 29 . . temp_limit_hi = 150 temp_limit_lo = -100 . . . . temp_limit_hi_max = 160.0 temp_limit_hi_min = 20.0 temp_limit_md_max = 50.0 temp_limit_md_min = -40.0 temp_limit_lo_min = -110.0 . . . .
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vt_pid_std_nb_h_pb = 1.3 vt_pid_std_nb_h_ti = 29 vt_pid_std_nb_h_td = 5 vt_pid_std_nb_h_cbl = 10.0 vt_pid_std_nb_h_cbh = 0.0 vt_pid_std_nb_h_hc = 2.4 vt_pid_std_nb_h_hl = 70 . . (Other "vt_pid_" values not shown here for brevity.) domain 1H 90 = 10.4 18 50 probe_tune = 0000 probe_match = 2625 end 1H domain 13C 90 = 8.3 8.2 39 probe_tune = 2770 probe_match = 5145 probe_coarse = NONE end 13C domain 29Si 90 = 10.2 10.2 40 probe_tune = 5040 probe_match = 4860 probe_coarse = A end 29Si domain 31P 90 = 7.6 7.6 38 probe_tune = 4870 probe_match = 5390 probe_coarse = X end 31P domain 15N 90 = 14.7 14.7 60 probe_tune = 3500 probe_match = 2745 probe_coarse = E end 15N end probe
Note: The values in the program above specify the temperature PID parameters for this probe when operating in various modes.
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The std. qualier species STANDARD duration VT control. The long qualier species LONG duration VT control. The nb qualier species NARROW magnet bore. The wb qualier species WIDE magnet bore. The _h_ qualier species HIGH temperature operating range. The _m_ qualier species MID temperature operating range. The _l_ qualier species LOW temperature operating range. The _0_ qualier species 0-DEGREE-C offset mode. The _40_ qualier species -40-DEGREE-C offset mode. Explanation of xxxx.probe le entries: probe This eld is used to describe what types of nuclei and experiments for which the probe can be used. These include, but are not limited to: 5mm_Broadband, 5mm_C/H, 10mm_Broadband, Tunable, C/H, Autotune, HX, Proton, 1H, Carbon, 13C, 19F, and Fluorine. This eld denes the default irradiation code for the 1H decoupler. The meaning of this code can be found in Chapter 10. This eld denes the default 90 pulses for nuclei not explicitly dened in the xxxx.probe le. The rst value is the observe 90 pulse width, the second value is the high power irradiation pulse 90 width used for polarization transfer experiments, and the third value is the decoupling 90 pulse width used for pulse decoupling sequences. This eld is the proton 90 pulse width for spin-lock and isotropic mixing experiments.
irr_code
90
spin_lock_90
spin_lock_attn
This eld is the proton channel attenuator setting for spin-lock and isotropic mixing experiments.
temp_limit_hi temp_limit_lo
These elds indicate the temperature limits of the probe. Delta will not allow these limits to be exceeded.
domain X ... end domain
These entries are used to dene the scope of parameters used for a specic nucleus. Entries for a particular domain are used only when that nucleus is used in an experiment. Denes the default probe tune values for tuning the nucleus specied by the current domain.
probe_tune
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probe_match
Denes the default probe match values for tuning the nucleus specied by the current domain. Denes the coarse probe tune value for tuning the nucleus specied by the current domain. This can be either a specic probe tuning stick on a broadband probe or the dial position on an autotune probe. HF is used to select the proton / uorine channel for the autotune probe.
probe_coarse
Note: Other machine parameters may also be dened for a specic domain. These have the same form as the parameters contained in the machine action les. xxxx.shims This le contains the standard system-wide shim settings for the probe. These can be updated by connecting to the Eclipse NMR spectrometer as console and using the Save System Shims in the pull-down menu. Only users connected as console may update this le. xxxx.shims.0 This le contains the system shim le prior to the current one. xxxx.limits This le contains the tuning limits for the dials on an autotune probe. Do not change the values in this le, the autotune probe will be damaged! xxxx.dials This le contains the current values for the dials on an autotune probe. This le is created and updated by the Cong Autotune Probe Tool on the Spectrometer Control Tool. /eclipse/shapes/ This directory contains les that numerically describe functions used in certain types of NMR experiments requiring RF shaping, or magnetic eld gradient control. Each le is an ASCII text list of up to 1024 oating-point numbers used by the acquisition system to selectively attenuate an RF signal (as in an experiment requiring RF shaping), or to create a time-varying magnetic eld gradient. There are two types of shape les: xed and user-denable. The user-denable shape les must be created with the names user0.shape through user9.shape. A userdenable shape le can contain from 3 to 1024 oating-point numbers.
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When an NMR experiment requiring RF shaping or magnetic eld gradient control is run, the acquisition system splines a smooth curve to t the data in the.shape le and applies this function to the shaped pulse in the experiment. The shaped curve will represent the smoothest curve possible within the time constraints of the shaped pulse's duration. eburp1.shape eburp2.shape gauss.shape iburp1.shape iburp2.shape left_half_gauss.shape user0.shape /eclipse/ Program Files aqp_program This le is the program that is loaded into the acquisition processor to control the data acquisition rates and sizes. cong_modem.sh This program is run by the installation program to congure and initialize the modem. control_aqp2, control_aqp3 This program controls all the Eclipse NMR spectrometer sub-systems including the acquisition processor, the pulser, the slow I/O peripherals, the Disk I/O, and the communication with the host Delta workstation. Help output from the control program: ./control [-hfqmprivn] -h Display this message -f Disable Powerfail experiment recovery -q Disable experiment logging -m Disable machine logging -c Disable machine communications -p Disable Loading pulser -r Disable Power on reset -i Disable idle lock on startup -v Display Version -n Do not start left_half_sinc.shape left_half_sine.shape ramp_down.shape ramp_up.shape reburp.shape right_half_gauss.shape right_half_sinc.shape right_half_sine.shape seduce.shape sinc.shape sine.shape uburp.shape
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Switches: -h Displays the list of switches for control and a short description of each switch's function. -f Disables the powerfail experiment recovery. Prevents any experiments remaining in the queue when control was terminated from automatically restarting. -q Disables the logging of experiment sample messages to the queue.log le. -m Disables the logging of spectrometer messages to the machine.log le. -c Disables communications with the SCON module, the slow I/O peripherals, and the pulser. -p Disables the loading of the pulcon.pul program into the pulser. -r Disables the power on reset of the spectrometer modules when control is started. -i Disables the machine.idle_lock action le. -v Displays the version information for the Control program. -n Causes control to load, execute the v switch if present and exit. eclipse This le is a Bourne shell script le run at boot time. It will restart Control if it crashes due to a hardware or software failure. Sample eclipse script le: #!/bin/sh exec >/dev/null 2>&1 cd /eclipse HOME=/ export HOME if /sbin/chkcong aqp2; then npri -h 30 /eclipse/control_aqp2 >/dev/null 2>&1 while /bin/true; do npri -h 30 /eclipse/control_aqp2 -p >/dev/null 2>&1 done else npri -h 30 /eclipse/control_aqp3 >/dev/null 2>&1 while /bin/true; do npri -h 30 /eclipse/control_aqp3 -p >/dev/null 2>&1 done gxscon.scn This le is used for Eclipse spectrometer initialization when the spectrometer is power on. machine.alarms This le contains a listing of the possible alarms generated in the Eclipse
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spectrometer due to a hardware failure. machine.authorization This le controls a user's access to machine features, and consists of a user name followed by a list of restrictions. make_copy This program is used to make a copy of a currently running experimental data le and upload it to Delta. The make_copy program allows for the monitoring of an experiment's progress. pulcon.pul This le is the pulser control program. It is downloaded to the pulser when the spectrometer is powered on. /usr/eclipse/ This directory contains log les that result from machine operation and data les waiting to be uploaded to a Delta workstation for processing and display. cryogen.log This le contains a log of the cryogen levels in the instrument. machine.log This is the instrument log le. It contains all the messages that are normally printed on the Delta Console for this instrument. It also contains additional information about hardware errors that may be occurring in the Acquisition System. machine.old This is the second most recent machine.log le. The machine.log les are restarted on a schedule dened in the machine.cong le. New logs start with the rst entry after midnight on the day dened in the machine.cong le. queue.log This is the current sample log for the instrument. It contains entries for each sample that was run. This le also lists which user ran the experiment, when the experiment was run, how long the experiment was scheduled to take, and how long the experiment actually took.
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queue.old This is the most recent queue.log le. The queue.log les are restarted on a schedule dened in the machine.cong le. The new logs are started with the rst entry after midnight on the day dened in the machine.cong le. /usr/eclipse/testprogs/ These programs and les are used for testing the Eclipse acquisition hardware. blink.cof This le is downloaded to the Acquisition Processor with the download program. If the download is successful, the user light on the Acquisition Processor will blink until the program is terminated. count This program will determine the number of Acquisition Processors installed in the Acquisition System VME Chassis. download This program is used to download Acquisition Processor *.cof les and start program execution. hw_debug This program is a spectrometer hardware-debugging utility for use by eld service engineers only. Warning: Only service engineers can use this utility, and JEOL is not responsible for any damages incurred by using it. ident_sipp This program is used to test the memory of the AQP-III Data Acquisition Board. interrupt.cof This le is downloaded to the Acquisition processor with the interrupt_test program. interrupt_test This program tests the VME interrupt handshaking between the Acquisition processor and the SGI V35 CPU. Count is the number of times required to run the interrupt test. Value is the number loaded into the Acquisition Processor to test
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specic values for data transfer. Help output from the interrupt_test program: ./interrupt_test count coff_filename [value] test_lights This program will test the indicator lights on the front of the Acquisition System chassis. test_serial_ber This program is used to test the Serial Fiber Optic connection board. This test requires a ber optic loop-back cable. /etc/init.d local This le is used to automatically start the eclipse script when the system is booted.
#!/sbin/sh #Tag 0x00000f00 case "$1" in `start') rm -rf /lost+found/* /eclipse/eclipse & ;; `stop') killall eclipse control_aqp2 control_aqp3 ;; *) echo "usage: $0 {start|stop}" ;; esac
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SAMPLES
APPENDIX F: DESCRIPTION OF THE AUTOMATION TEMPLATE FILE

An Automation Template file is a ASCII file generated by the Automation Editor (see below) and read by the Automation program. The template file contains instructions for a spectrometer to carry out one or more experiments. This description is intended to give the user an understanding of what the template file contains. There are two main categories of instructions in a template file. A SAMPLE statement and a METHOD section. There may be more than one of each, and they may be written in any order. In some instances, Methods may depend on Samples that have been defined with the SAMPLE statement. In these cases, the SAMPLE definition must precede the METHOD section that depends on it. In this short overview, items placed in brackets, [ ], will be considered optional items for the syntax and may be omitted. Items separated by a vertical bar indicate that a choice must be made for one item only.
SAMPLES
Samples are useful for declaring sets of named attributes for which an experiment will be run on. Declaring more than one Sample and including the titles in the GROUP section allows repetition of experiments without having to write an Experiment declaration for each Sample for which you'd like to collect data. Here is an example of a SAMPLE statement: SAMPLE sample_name IS SAMPLE_ID"001_56" [COMMENT"This is a test sample"] SLOT 2 SOLVENT"CHLOROFORM-D"; The words which are capitalized and not in quotes are keywords. Sample_name is the title given to this group of sample attributes, namely the sample_id, comment, slot to run on, and solvent to use. The comment field may be omitted in which case it will be set to "". See the EXPERIMENT definition for a description of each of the four attributes.
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METHODS
The Method section is defined as follows: METHOD method_name IS [ADVANCED] [PRINTER "my_printer"] [HELP "This is the help text"] GROUP... . . END GROUP; . [ <more groups> ] END METHOD; The keyword ADVANCED on the first line of the METHOD section is optional. If it is omitted, then the experiments contained within this Method will run immediately when submitted. If the Method is declared to be advanced (by including this keyword after the IS), then when the Method is run, a pop-up box will appear allowing the user to modify many of the values of the experiment parameters. This will not be discussed further here. The second line beginning with the keyword PRINTER is also optional. The printer entry defines the printer for which the experiments in this method will be plotted. Entries must exist in the .delta_configure file for this to work properly. If any or all of the entries cannot be found in the .delta_configure file, then the default printer and settings will be used for the missing entries. The third line beginning with the keyword HELP is optional as well. It defines a help label that will appear on the button labeled with the Method name. It is a string, or more than one string separated by commas.
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GROUPS
GROUPS
Inside the METHOD section is at least one GROUP section. The GROUP section contains one or more EXPERIMENT definitions, and some other optional information. This section may seem a bit unnecessary, but when repetition is required (especially over many different samples) it immediately becomes clear that a grouping of experiments is needed. A GROUP section is defined as follows: GROUP group_name [USINGTest_Sample] [EXECUTE"program_name"] [BASENAME"base_filename" mode] IS EXPERIMENT... . . END EXPERIMENT; . [ <more experiments> ] [PRESENTATION "presentation_file" FOR list_of_box_definitions; . [ <more presentations> ]] END GROUP; The optional USING keyword is followed by a Sample name (defined by a SAMPLE statement described above), or a list of Sample names separated by commas. This causes each experiment in the Group to be run once for each Sample that is specified. The optional EXECUTE keyword is followed by a single string which is the name of a Percival program to run when the Group of experiments has all been collected. There is a specific parameter passing scheme that must be followed, but this is beyond the scope of this description. The optional BASENAME keyword is followed by a single string which is concatenated with the sample_id and the optional EXTENSION found in the EXPERIMENT declaration to form the filename of the experiment stored on disk. The string is then followed by a mode indicator. This mode indicator can be either fixed or runtime. See the Mode Indicator Table at the end of this description for information on the different modes certain parameters may have.
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EXPERIMENTS AND PRESENTATIONS

Experiments and Presentations may be defined in any order, mixed or otherwise. However, since Presentations require Experiments to be defined for useful operation, it is required that Experiments required for a Presentation must be defined before the Presentation statement. It is a good idea to define all Experiments first, then define all Presentations at the end. Doing this avoids much of the hassle of figuring out where to put the definitions. Experiments Inside each GROUP section is one or more EXPERIMENT declarations and zero or more PRESENTATION statements. A simple EXPERIMENT declaration is defined as follows: EXPERIMENT experiment_name IS [EXTENSIONextension_text] [SAMPLE_IDid mode] [COMMENT comment_text mode] [SLOT slot_number mode] [SOLVENT solvent_name mode] [TEMPERATURE[temp mode] [ON|OFF mode]] [SHIM shim_file_filename] [PROCESSINGprocess_list_filename] EXP_FILE experiment_file_filename; END EXPERIMENT; The optional EXTENSION keyword is followed by a string which is appended to the filename of the experiments that will be stored to disk. The optional SAMPLE_ID keyword is followed by a string which is the identification string of the experiment. This string forms the first part of the experiment's filename. Mode can be any of the three possible modes. Refer to the end of this discussion for what each mode means. The optional COMMENT keyword is followed by text which forms the comment/ description for the experiment. Mode can be any of the three possible modes. Refer to the end of this discussion for what each mode means. The optional SLOT keyword is followed by a number indicating which slot to find the sample in if you have an automatic sample changer. If this is defined as a number but no sample changer is present, this option is ignored. Mode can be any of the three possible modes. Refer to the end of this discussion for what each mode means. The optional SOLVENT keyword is followed by a string which names the solvent which exists in the sample. Mode can be any of the three possible modes. Refer to the end of this discussion for what each mode means.
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EXPERIMENTS and PRESENTATIONS
The optional TEMPERATURE keyword is followed by one or both of the following temperature definitions in either order: 1) A universal number with temperature units to set the temperature value followed by a mode indicator. 2) The keyword ON or OFF to set the temperature state followed by a mode indicator. Mode may only be fixed or runtime. The optional SHIM keyword is followed by a string which is the filename of a file that contains shim information for a spectrometer. Mode may only be fixed or runtime. Refer to the end of this discussion for what each mode means. The optional PROCESSING keyword is followed by a string or a list of strings which are separated by commas. Each string is a path and filename of a processing list which the experiment will be processed with after it has been collected. The EXP_FILE keyword is a string which is the filename for the experiment file that will be used to run the experiment. A more detailed EXPERIMENT has the form like the following: EXPERIMENT experiment_name IS <all optional parameters as above> EXP_FILE experiment_file_filename DO parameter_name := parameter_value; . . [ <more parameter initializing> ] . TAKE [value comparator] parameter_name [ASSIGN_TO parameter_name] [comparator value] [CONSTRAIN multiplier [/ modulus]] [UNIT unit_val] . . [ <more take_parameters separated by commas> ] FROM experiment_name; END EXPERIMENT; This requires some explanation. Notice the semi-colon at the end of the experiment_file_filename has been replaced by the keyword DO. This indicates that there are some extra things we want to define about this experiment. It is possible to initialize experiment parameters and/or forward parameters from a previous experiment. First, we can declare and initialize any parameter to any constant value. For example, we may set scans equal to 32 or auto_gain to TRUE with the following statements respectively: scans := 32; auto_gain := TRUE; Second, we can define that a certain parameter or parameters be taken from a
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"previously" defined experiment. In addition, we can specify constraints on the parameter(s) of lower bound, upper bound, multiple of, and modulo of. In the TAKE section, value can be any constant parameter value. Of course, if it is not a legal value for that particular parameter_name, then maintaining this constraint will fail. Legal comparators are < (less than), <= (less than or equal to), > (greater than), and >= (greater than or equal to). It is possible to define these bound constraints in a number of ways. Here are some examples, including an unbounded parameter: TAKE TAKE TAKE TAKE TAKE TAKE TAKE x_sweep FROM ... x_sweep < 2[ppm] FROM ... 2[ppm] > x_sweep FROM ... (same as above) 1[ppm] <= x_sweep < 3[ppm] FROM... 3[ppm] > x_sweep >= 1[ppm] FROM... (same as above) 3[ppm] > x_sweep, y_sweep >= 1[ppm] FROM... x_sweep, scans FROM...
It obviously makes no sense to include bounds on the last TAKE statement above since the parameters do not have the same type of legal values. However, this is a legal statement and simply makes no restrictions on the values they may have -- they are just taken from the experiment specified with their current values. If it is necessary to constrain the value of a parameter to be a multiple of some number or the modulo of some number then the CONSTRAIN keyword must be used. After any and all bounds restrictions, the CONSTRAIN keyword is placed followed by a number that the parameter_value will be rounded to be a multiple of. If modulo is desired, include a forward slash next followed by a number for the modulus calculation. If modulus is desired, but no multiplier, a value of 1 (one) must be placed in the multiplier place. For example: TAKE scans CONSTRAIN 1 / 16 FROM... This would have the same effect as TAKE 0 <= scans < 16 FROM... However if the statement was TAKE scans >= 0 CONSTRAIN 4 / 16 FROM... then possible values for scans would be 0, 4, 8, and 12. To enforce units on a forwarded parameter, use the UNIT keyword. For example: TAKE x_sweep UNIT [ppm] FROM... would convert x_sweep to ppm units before passing it to the next experiment. CONSTRAIN and ASSIGN_TO can also be used with the UNIT keyword. As in: TAKE scans >= 10 CONSTRAIN 2 / 100 UNIT [] FROM... This would enforce scans to be great than or equal to 9, be an even number less than 100, and have no units.
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EXPERIMENTS and PRESENTATIONS
It is also possible to forward a parameter from an experiment to a different parameter in the next experiment. This is done with the ASSIGN_TO keyword. Here are some examples: TAKE x_sweep ASSIGN_TO y_sweep FROM... TAKE -3[ppm] <= x_sweep ASSIGN_TO y_sweep <= 3[ppm] FROM... Both of these commands take the parameter, x_sweep, and applies it's value to y_sweep. The second TAKE command simply adds constraints. Presentations As defined above, a PRESENTATION is declared as follows: GROUP group_name IS . . [PRESENTATION "presentation_file" FOR list_of_box_definitions; . [ <more presentations> ]] END GROUP; Notice that Presentation statements are optional. Thus, a Method need not have a plotted output. Of course, the data file will always be saved to disk regardless. A presentation_file is a path and filename for a presentation template file that was created by the Presentation Manager tool. To write this section, it requires that one know quite a bit about what the presentation template file contains. The list_of_box_definitions is exactly that: a list of box definitions. A box definition can be any of the following types: a named experiment, a NULL_DATA keyword, or a NULL_BOX keyword. There is a box definition for each box that exists in the template file separated by commas. The first box definition corresponds to Box 1 in the template. Likewise the second box definition corresponds to Box 2, etc. Describing the simplest first, NULL_BOX is a keyword indicating that a data file is not a parameter to this template for the box number of its position. Thus, if Box 1 in the Presentation template file is not a parameter box, then NULL_BOX would be the first box definition. NULL_DATA indicates that this box is indeed a parameter box, but no data file will be passed to it. It is necessary to place a number in brackets immediately in front of this keyword (leaving no spaces) to indicate the number of the parameter that this will go into. For example, [2]NULL_DATA indicates that there will be no data file passed as the second parameter. A named experiment consists of a number in brackets (like was done for NULL_DATA) followed immediately by the experiment_name. The number in brackets,
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as above, indicates which parameter will get this data file. If the user would like to display processed data, then immediately following the experiment_name (leaving no spaces) place a @_ followed immediately by an INTEGER which is an index into the list of processing_lists. For example, to place a processed data file using the second processing list into the fourth parameter of the template file one would write: [4]Exp_Name@_2 *** FILENAME NOTE *** An experiment's filename (the name that the collected data will be saved to) is created from three components. First, the SAMPLE_ID from the EXPERIMENT declaration, followed immediately by the BASENAME that is in the GROUP section, and finally followed by the EXTENSION taken from the EXPERIMENT declaration. The data file will also be assigned a version number. Mode Indicator Table A mode indicator can be one of the following: fixed, runtime, or sample. Refer to the following table for descriptions of each.
FIXED
A fixed mode indicator means that the value of that parameter cannot be changed when the experiment is run. This will be the case for Methods defined as NOT being an Advanced Method. A runtime mode indicator means that the value of that parameter may be changed just prior to submission given that the Method being submitted is an Advanced Method. A sample mode indicator means that the value of that parameter will take on the value(s) that is (are) defined in the Use Sample(s) parameter box for that Group. This will be the case regardless of the Advanced mode. The experiment will be run once for each sample.
RUNTIME
SAMPLE
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Logic of Flow in the Automation Editor
LOGIC OF FLOW IN THE AUTOMATION EDITOR

When the user first starts the Automation Editor with no automation template to load at start-up, the user is presented with a blank screen. Before any Experiments may be added to the file, a title for the Method must be supplied. The Group will automatically be titled with the same name as the Method, but the user may change either title. Following these one or two steps, Experiments may then be defined. It is recommended that you create any Sample definitions first, followed by creating the Experiments, and lastly supplying Presentation information. It is not necessary to define the Samples first, but it is required that Experiments be defined before Presentations. It is possible to define Experiments that do not have Presentations (no printer output), but not vice versa. In a basic Method, the only necessary line to fill in (besides the Method, the Group, and the Experiment titles) to define an Experiment is the Experiment File line. Without an experiment file, the experiment cannot run. Every experiment in every Group will be run once on the Spectrometer. If Samples are used in the Group, i.e. the Use Sample(s) field has one or more Sample titles in it, then only the experiments in that Group will be run once for each Sample specified. Parameters can be initialized for any Experiment and they may only be initialized to constant values. For example, you CANNOT define the following: filter_start := 1[ppm]; filter_stop := filter_start + 1[ppm]; In this case, filter_start will be set correctly, but filter_stop will be set to the string "filter_start + 1[ppm]". Obviously not what was intended. You must specify the above initialization as: filter_start := 1[ppm]; filter_stop := 2[ppm]; Forwarded parameters may only come from a previously defined Experiment. The order in which the Experiments appear in the list box is the order in which they will run on the spectrometer. In a way, Forward parameters are like Initialize parameters except that they get their initial values from an experiment rather than from a constant user set value.
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APPENDIX G:
PRESENTATION MANAGER AND
TEMPLATE FILE FORMAT

CONSOLE COMMANDS
A unary operator called pm does the bulk of Presentation Managers work. It is possible to call pm from processing lists, the command line, and percival code to aid in the automation of plotting. The following is a description of how to call pm. The Presentation Manager kernel is an operator called pm. To facilitate the automation of plot output, this operator can be called from the command line, a percival program or operator, or a processing list. There are four execution modes associated with pm. Execution mode 1 is for executing a template le, 2 is for reading a template le, 3 is for executing symbolic information, and 4 is for writing symbolic information to a template le.
pm 1: template_file :: VT_FILE [: runtime_files :: (VT_FILE, VT_SET) [: plot_parameters :: VT_SET ]] pm 2: template_file :: VT_FILE pm 3: symbolic_info :: VT_SET preview_boolean :: VT_BOOLEAN : plot_parameters :: VT_SET :
pm 4: symbolic_info :: VT_SET : template_file :: VT_FILE
The runtime les in execution mode 1 correspond to parameter numbers specied in the template le. These numbers are designated in le variables, and appear in the form P#, where # is the number of the le that will be referenced from the runtime_files set. For example, if le1 in a template le references parameter 3, then runtime_files should be at least a three element set, and le1 refers to the third element in that set. If only one parameter number is specied in the template, then runtime_files may be a le instead of a set of les. The plot_parameters argument in execution modes 1 and 3 should be of the form:
[queue :: VT_BOOLEAN, delete_file :: VT_BOOLEAN, file_name :: VT_STRING, plotter :: VT_STRING, paper_size :: VT_STRING, color :: VT_BOOLEAN, output_orientation :: (WM~LAND|WM~PORT), tesselation_value :: VT_NUMERIC}
For execution mode 1, if no runtime les are to be specied, but plot_parameters is going to be specied, an empty set should be placed as the second argument. For execution mode 3, if plot_parameters is not going to be specied, then an empty set
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should be used in its place. The symbolic_info argument referred to above should be of the form:
{{position :: VT_SET, type :: VT_STRING, features :: VT_SET, attributes :: VT_SET, data :: VT_SET, processing_list_file :: VT_STRING, ruler_info :: VT_SET}...}
A sample template File (.pmt) The following sample le describes a single, full-size box. The geom indicates that this box will display data. The empty sets indicate that defaults are to be used for features and attributes.
[box] box1: {0[%], 0[%], 0[%], 0[%]} : geom : {}:{} [file] file_1 : /usr/files/data/1d/1heb.1 [process_lst] process_lst_1 : /usr/files/process_lists/reverse.lst [transformation] file_1 => process_lst_1 => box1 [ruler] box1: X : 100 : 0
[end]
The le variable file_l is assigned a literal string, referring to a data le called 1heb.1. The processing list variable process_lst_1 is assigned a processing list le called reverse.lst. The transformation section species that process_lst_1, and then displayed in box1.
file_1
is to be processed using
The ruler section indicates that box 1s x-ruler will be set to 100 at the upper bounds, and to 0 at the lower, in whatever units the le is in. Comments may be placed in the template les. Any text following -- will be ignored.
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APPENDIX H: TERMINAL CONSOLE PROGRAM

The terminal console program allows you to communicate remotely to Delta through a terminal emulator. This allows you to remotely monitor spectrometers without a Silicon Graphics terminal. This feature is useful when you are running a lengthy experiment, or a series of experiments. It allows you to see what jobs are running, and to cancel a job if need be. Note: The terminal console program requires that a copy of Delta be running on the workstation. The terminal console program will only connect to Delta when it is run from the same UNIX account that started Delta. The copy of Delta running on the workstation does not need to be connected to a spectrometer; you make the necessary spectrometer connections from the terminal console program. For help on console, type: $ console -h To start the program, type: console [-r] [-l] [-e] [-w] [-p init_mode] [-n name] [- s number] [-h hostname] with or without any of the optional ags which are in brackets. where -r : Resets all client message ids and manages message passing -l : Lists all available servers -s : Selects a server by number -e : Line editor enabled (Default) -w : Without line editor enabled -p : Initial prompt mode, specifying mode of input -n : Requests connection by name -h : Connects to host Once a console program is running and connected to Delta, type: x_con to connect to the nongraphical spectrometer connection tool that has most of the same functions as the Delta Spectrometer Control Tool. This tool allows you to do the following (for clarication, see the discussion in Chapter 4): connect, disconnect or monitor a spectrometer access information on spectrometers and ascertain which spectrometers are free supply a password scroll the list of connected spectrometers show jobs abort a job or an entire queue
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start a job.
The screens below illustrate the menu of choices described above:
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APPENDIX I: TOOL ICONS

Delta tools, when turned into icons, have identiable and distinguishable pictures to help you rapidly pick them out from the array on your screen.
Icon
Tool
Presentation Manager template
Pick tool
Phase 2D
Parameter tool
Get directory
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Icon
Tool
Delta console
Interactive base correction
Geometry tool
Console manager
File Math
Export
Import
Experiment tool
I-2
Icon
Tool
Reference
Dept/Inept
Calculator
Debugger
Data slate
T1 Analysis
Automation
Autoqueue
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Icon
Tool
Automation Editor
Connect
Chart
Cursor
Level
Automation
Line Editor
Parameter Editor
I-4
Icon
Tool
Preferences
Connection
Spectrometer
Spread Sheet
Signal/Noise
View Control
Transfer Integral
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Icon
Tool
Peak List
Parameter Viewer
3D Plotter
Widget Editor
Template
Window Phaser
1D Processor
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Icon
Tool
nD Processor
Process
I-7
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APPENDIX J: UNIX AND VI COMMANDS

This appendix lists Unix and VI commands frequently used in conjunction with running Delta.
I. UNIX COMMANDS
Command pwd Usage pwd Example Lets you know your present working directory; i.e., if you are in the delta account it will printout /usr/people/delta. Clears the screen. Changes directory to next higher directory in tree, cd .. when presently in /usr/people/delta results in the new directory being /usr/people cd. cd /usr/people/delta/files/data changes current directory to /usr/people/delta/files/data. cp /usr/people/delta/filename.x /usr/people/delta/files/data/, copies filename.x from /usr/people/delta/ to /usr/people/delta/files/data.
clear cd
clear cd ..
cd
cd [path]
cp
cp [from] [to]
mv
mv [from] [to] mv /usr/people/delta/filename.x /usr/people/delta/files/data/, moves filename.x from /usr/people/delta/ to /usr/people/delta/files/data. rm [filename] rm filename.x removes filename.x from the current directory. Wildcarding is supported, i.e., rm file* removes all les that have the name le. df -k ls -la Displays disk space in kilobytes. Lists all les including hidden les. Hidden les have the format .lename (period before lename). Lists les by date in descending order.
rm
df ls
ls
ls -ltr
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tar cv
tar cv *
Tape archival of les from disk. Files in the current directory and all sub directories are archived. Tape archival with append. Files can be appended to previously archived les using the tar cv command.
tar rv
tar rv *
tar xvtar xv [filename]Extracts les from tape back to disk. Without an argument all les are restored. A lename argument restores a specic le. tar t tar t Lists contents of a tape made using tar.
ls > test.txt
ls > [filename] ">" stands for pipe. Normally ls would list les on the CRT. By using > the le listing is piped to a diskle. A lename must be supplied. The pipe can be used in all cases when an output is being generated.
mkdir mkdir [directory name] Creates a subdirectory.
II. VI COMMANDS
Command x i a : wq! q! Deletes a single character. Inserts. Must be followed by an escape key stroke to exit insert node. Appends to the end of a line. Must be followed by an escape key stroke. Starts command line. Before the wq! and q! Writes the current le and quits. Quits VI without saving the changes.
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APPENDIX K INSTALLING JEOL AUTOTUNE PROBES

This appendix describes the procedures for installing JEOL AutoTune probes on Eclipse NMR spectrometers. 1. Turn off the spectrometer power. 2. Connect AutoTune controller box to B-Bus. This may be done directly to the spectrometer motherboard or in series with the sample changer. DO NOT connect the speedometer cables to the probe. 3. Plug the Autotune controller into 120V; there may be two 120V plugs. 4. Power on the spectrometer, acquisition system, and AutoTune controller (two switches). The system should come up as normal. Login and run Delta. 5. Open a terminal shell and login into the acquisition system as root. 6. If the AutoTune probe is being installed for the rst time, the 2564.probe le must be checked for the correct entries. For each nucleus the COARSE, TUNE and MATCH values must be veried. After running the specications, you should have written down values for 1H, 13C, 31P, and 15N. If other nuclei are desired, the probe must be manually tuned to the nucleus and the values entered in the 2564.probe le before automatic probe tuning is attempted. Write the values here: Nucleus - COARSE - TUNE - MATCH 1H - HF 19F - HF 31P 13C 15N 7. Type cd /eclipse/probes 8. Type ls The les for the standard TH5 autotune probe (probe id 2564) are: 2564.shims 2564.probe 2564.limits 2564.dials The .shims and .probe les should already exist. If they do not exist - STOP
now - you have not installed the probe correctly.

The .limits le may exist but must be veried before installing the autotune probe. The .dials le should not exist yet. 9. Edit the 2564.probe le with vi and place the recorded COARSE, TUNE and MATCH values for the nuclei in the correct domain sections. Save the le and exit vi. You may have received a printout of a probe le with the probe. Do not assume those numbers are correct, every nucleus must be veried in installation by manually tuning the probe. 10. The 2564.limits le must be veried. On the probe, turn the LF TUNE, LF MATCH, HF TUNE, and HF MATCH knobs to their minimum values. Write these numbers
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down. Turn the same knobs to their maximum values and write the numbers down. DO NOT FORCE THE DIALS. As soon as there is any turning resistance, the end has been reached. LF TUNE LF MATCH HF TUNE HF MATCH 11. Edit the 2564.limits le to match these veried limit values. Change the values in the le to match the measured values. If the le does not exist, create a le with vi. After editing the le, save it to disk and exit vi. The format of the .limits le is: LF TUNE minimum LF TUNE maximum LF TUNE step size (default 10) LF MATCH minimum LF MATCH maximum LF MATCH step size (default 10) HF TUNE minimum HF TUNE maximum HF TUNE step size (default 10) HF MATCH minimum HF MATCH maximum HF MATCH step size (default 10) For example: 150 4500 10 200 2800 10 150 1100 10 160 2750 10 12. Connect the cables to the Autotune probe. There are 5 cables LF COARSE, LF TUNE, LF MATCH, HF TUNE, HF MATCH. These are color-coded on the collar. You may need to gently jiggle the knobs to engage the worm gears. Be careful, don't force the gears. 13. Connect to the instrument via Delta in Console mode. 14. From the spectrometer control window, select the PreTune button, 15. Fill in the blanks on the screen by reading the dial values. Make sure you get the order correct, and do not assume they are where you left them because they will change when the cables are connected.
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Probe Tuning
16. Save the .dials le by clicking the button. A message should be displayed in the Master Console. 17. Unlink from the spectrometer and reconnect as normal. 18. Submit a single_pulse proton experiment. Watch closely in the Master Console, messages regarding tuning will be displayed. 19. If all is well, the probe will initialize itself by checking the 31P tuning. This is how it nds the COARSE position (X, A, B, C, D). If there is an error, a message will be printed in the Master Console. The most common error is Dials le not found. In this case, re-connect as console and save the dials le again, then re-boot the acquisition unit. The presence of the dials le can be veried by rlogging into the acquisition system and looking in /eclipse/probes. To prevent damage to the probe, the dials le is deleted while the probe tuning is in motion. Therefore it may appear and disappear. 20. After initialization, the probe will tune for the requested nucleus in the experiment, in this case 1H. 21. The probe should reinitialize itself properly each time, if there is a dials le present. If no dials le is found, a message will appear in the Master Console, and the system manager must create a new dials le with the PreTune button.
PROBE TUNING
Probe Tuning is performed using the probe_tune experiment in the global experiments directory. The probe_tune experiment uses very low power RF and a directional coupler to adjust the probe tuning. To tune a probe: Load the probe_tune experiment from the global directory. Set the desired nucleus for tuning, and submit the experiment. If you are tuning a current generation probe with digital tuning readout, nd the tuning sheet for the probe and dial in the standard values for the nucleus you are tuning. If you are tuning the broadband channel, nd the correct tuning capacitor stick on the sheet and insert the capacitor into the probe. Note: make sure that any existing capacitor sticks are removed from the probe if they are not required. Using the level knob and the x10 button, bring the meter to 50% scale. Use the Tune knob to minimize the meter deection. The Tune knob will be different for the HF and LF channels. On some probes, the HF Tune is a small red knob without a digital readout. The LF tune is usually a digitally encoded knob. Be certain you are turning the correct knob. If the meter deection decreases to a value too small to see on the meter, use the level knob or x10 button to increase the deection. When a minimum is found with the Tune knob, move to the Match knob, if there is one for the channel you are tuning. Not all probes have Match knobs for all channels. If the probe channel you are tuning does not have a Match knob, move the Match knob to nd a minimum on the meter. Now that you are at the minimum, move the Match knob one direction to increase the meter deection. Remember the direction you
1. 2. 3.
4. 5.
6. 7.
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turned the knob! 8. Turn the Tune knob to minimize the deection again. If the new minimum deection is lower than the previous minimum deection, then the Match knob was moved in the correct direction. If the new minimum deection is higher than before, then the Match knob was moved in the wrong direction. 9. Continue this process iterating between the Tune and Match knobs until the best minimum is found. As a general rule, a clockwise movement of the Tuning capacitors will tune to a higher frequency. 10. If this is the rst time the probe is being tuned to a nucleus, write down the Tune and Match values on the tuning sheet or roadblock. 11. Terminate the probe_tune experiment from the spectrometer queue. Before running an NMR experiment on an Eclipse system, conrm that the BNC cables are correctly connected. Running an NMR experiment with the cables left in the probe tuning conguration will damage the directional coupler.
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APPENDIX L: DELTA V3.2 SOFTWARE INSTALLATION AND CONFIGURATION INSTRUCTIONS

This appendix describes the procedures for installing and upgrading the Delta software and the Eclipse control software, and for setting up new user accounts. Portions of this document contain Year 2000 information and is covered by the Federal Year 2000 Readiness and Disclosure Act enacted October 19, 1998, for more information please contact your local JEOL office. JEOL USA Year 2000 compliant products are provided under the standard JEOL USA terms and conditions of sale, license, and support.
I. SYSTEM REQUIREMENTS FOR DELTA V3.2

Delta V3.2 supports several additional workstation and acquisition systems. These are outlined below, for more information please contact your local JEOL ofce. Workstations: SGI - IRIX: See sections III and IV for installation or upgrade instructions. Indy R4xxx, R5xxx - any graphics level Indigo R4xxx - XS, XS24, XZ or Elan graphics Indigo2 R4xxx, R5xxx- XZ, Extreme, or Impact graphics O2 R5xxx, R10K - any graphics level Octane - any graphics level All systems with minimum 64 Mbyte RAM (128 Mbyte for O2 & Octane) Either IRIX 6.2, 6.3 and 6.5.x operating system on the workstation. Note: Version 3.2 is not supported for IRIX 5.x and earlier on the workstation. CD-ROM drive Note: SGI IRIX 6.2 and 6.3 require Y2K patches, to obtain a the Y2K patches for SG IRIX version 6.2 o 6.3 please contact JEOL. Intel - Linux See sections V and VI for installation or upgrade instructions. Intel Pentium II, 400 MHz or faster RedHat Version 6.2 Linux XFree86 V3.3.5 or Xi Graphics V1.1 3D Accelerated-X Drivers 256 Mbyte Memory Ethernet Network card for license key. CD-ROM drive Note: JEOL has tested the following congurations: Pentium II-450, Pentium III-733, Pentium III-800, with Evans & Sutherland Lightning 1200, Matrox G400, 3Dlabs Oxygen GVX1, 3Dlabs Oxygen VX1, ATi Radeon 64MB. Note: Please contact JEOL to discuss Linux system congurations and performance levels.
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IBM - AIX See sections VII and VIII for installation or upgrade instructions. IBM RS/6000 Power PC workstations with 24 bit graphics AIX Version 4.3.2 or 4.3.3 with the latest patches 256 Mbyte Memory CD-ROM drive Note: JEOL has tested the following models: 140, 150, 260 with GXT 550, GXT 2000, GXT 3000 Graphics Boards Sun - Solaris See sections V and VI for installation or upgrade instructions. Sun UltraSPARC 10 workstations with 24 bit graphics Solaris Version 8 with OpenGL, October 2000 release 256 Mbyte Memory CD-ROM drive Note: JEOL has tested the UltraSPARC 10 with Creator 3D, Elite M3 and PGX 24 graphics boards. Delta V3.2 uses the same software license key as previous versions of Delta, if you are upgrading you do not need a new key for Delta. Acquisition Systems: Delta V3.2 supports all acquisition systems with the SGI Indy computer running SGI IRIX V5.3. Version 3.2 is not supported for SGI V35 acquisition systems running IRIX V4.0.5, however Delta V3.2 will communicate with and run experiments on V3.1.2 V35 based acquisition systems. To update the acquisition system to Delta V3.1.2 please see section IV-c after installing Delta V3.2. NMR Spectrometers: Delta V3.2 supports the following NMR spectrometer hardware: Eclipse+ NMR spectrometer Eclipse NMR spectrometer Delta Upgrade for GX, GSX, CPF, EX and Lambda spectrometers Delta V3.2 is installed from CDROM using the SGI Software Manager tools or install scripts for the Linux, AIX, and Solaris versions. Please nd the appropriate section to install Delta on your system.
II. PREPARING FOR THE DELTA V3.2 SOFTWARE INSTALLATION OR UPGRADE
Note! Check the system requirements for your system before attempting to install Delta.
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III. Installing or Upgrading the Delta Software on SGI IRIX Systems
The Delta software package for processing NMR data is supplied on CDROM. The installation tools will install Delta into /usr/delta/. The Delta Software CDROM contains: the Delta NMR Processing Software, Standard Example NMR Data for Delta, the Delta Software Manuals in Adobe Acrobat (PDF) format, the Adobe Acrobat Reader V4.0, and several shareware PC / MAC programs that we have found useful. The PC and MAC programs are supplied as a courtesy without warranty or support. The manuals on CDROM can be accessed by opening the CDROM desktop folder and clicking on the appropriate icon. General notes: Delta requires Netscape Navigator and Adobe Acrobat Reader to access the help files. Netscape Navigator must be installed before installing Delta. Adobe Acrobat Reader is also required to view and print the Acrobat format manuals on the CDROM. The Adobe Acrobat Reader can be installed as part of the Delta installation procedure. When installing Delta for the rst time you will need to have a permanent Delta License Key. To obtain a Delta License Key install Delta and type /usr/delta/global/ verify to list the Delta Machine ID for new installations. Fill out the Delta License Key request form and FAX the form or e-mail the information to JEOL USA, Inc. You should receive a permanent Delta License key back within 2 weeks. The Delta software has a 60 day grace period from the time of manufacture before it will check for the Delta License key. Copies of Delta delivered after the 60 day grace period should include a 60 day temporary Delta License key.
Important! Please read the release notes for Delta V3.2 before starting the installation. Instructions to access the release notes are in the CD booklet. Note: Please read and understand all instructions before starting installation.
Note: The steps for installing Delta or upgrading the acquisition system are outlined below. Bold text is to be entered by the user. Bold text indicates a button or menu option that the user is to select. Click indicates a mouse action. Enter at the end of each line is assumed unless stated otherwise.
III. INSTALLING OR UPGRADING THE DELTA SOFTWARE ON SGI IRIX SYSTEMS

There are 6 major parts to the complete Delta NMR software package for SGI IRIX systems:
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Table N-1: Delta NMR software package components Component Name Delta Webserver Delta [v3.2] (Network License) Delta [v3.2] (Nodelock License) Delta [v3.1.2)] Eclipse Software for IRIX4 Delta [v3.2)] Eclipse Software for IRIX5 Delta [v3.2] NMR Data Processing Package 1. 2. 3. 4. 5. Description Delta Web interface to submit experiments Floating network Delta Software license. Requires a special license key. Standard Delta node locked software license. Installation Status optional optional standard
IRIX v4.0.5 files for Eclipse and Delta-UPG optional NMR spectrometer computers. This is the Delta V3.1.2 kit. IRIX v5.3 files for Eclipse and Delta-UPG optional NMR spectrometer computers. Support files necessary for the Delta NMR required Software package to operate correctly. standard
Login to the system(root) account. Insert the Delta Software CDROM into the CDROM drive. Double Click on the CDROM icon to open the desktop CDROM Folder. Double Click on the Install_Delta icon to start the SGI Software Manager. The Software Manager window will now appear. Note: Only the Software products and Software subsystems selected with the red check mark in the Install buttons will be installed.
6. Click on the Custom Installation Button. 7. Click on the Install button for the Delta Software License type that is correct for your system. The Delta NMR Data Processing Package and the Delta (Nodelock License) software are installed by default. Turn off the Delta (Nodelock License) if you are installing the Delta (Network License). Note: Only the Delta (Nodelock License) or the Delta (Network License) will install. Swmgr will generate a conict if you try to install both subsystems. Note: The Delta (Network License) software will not work with Delta (Nodelock License) keys. 8. Click on the Install button for the Delta [v32] Eclipse Software for IRIX if you have an Eclipse or Delta-Upgrade NMR Spectrometer Acquisition system. Choose the IRIX version (IRIX 4.0.5 or IRIX 5.3) that is correct for your acquisition system. 9. Click on the Install button for Adobe Acrobat Reader if Adobe Acrobat is not installed on your system and you want to view the Acrobat Format les on the
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IV. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System from an SGI Workstation
CDROM or use the Delta help les. 10. Click Start to begin the Delta Software installation. 11. The SGI Software Manager will now install the Delta software sub-systems selected. The install process will also identify any running Eclipse or Delta-Upgrade NMR spectrometers and set up an .rhosts le in the guest account, if the guest account is present, or in the root account, if the guest account is not present. The .rhosts le is used to install software on the acquisition system computer. 12. After the software installation has completed click OK to acknowledge the completion of the installation process. 13. Click File/Quit on the pull down menu or type <Ctrl>Q in the Software Manager window to exit the swmgr program. 14. Close the CDROM folder. 15. Right Click on the CDROM Icon and select Eject CDROM. 16. Put the CDROM in a safe place for future use. 17. Follow the instructions included with the Delta License Key to install the Delta License key, if one is not already installed. 18. If you have an Eclipse+, Eclipse, or Acquisition System attached to your system, continue with section IV Upgrading an Eclipse+, Eclipse or Delta-Upgrade Acquisition System.
IV. UPGRADING AN ECLIPSE+, ECLIPSE, OR DELTA-UPGRADE ACQUISITION SYSTEM FROM AN SGI WORKSTATION
For Eclipse+, Eclipse or Delta-UPG Acquisition Systems with Delta Currently Installed Only! The steps to upgrade the acquisition system software are outlined below. A. Setup for Eclipse+, Eclipse, or Delta-Upgrade Acquisition software upgrade. 1. Upgrade the Host workstation as described above in section III. 2. Login to the system(root) account on the workstation, and create a terminal window. 3. cd /usr/delta/eclipse to change to the eclipse software directory on the workstation. 4. ./backup_spectrometer eclipse2 to start the conguration le backup script. The backup_spectrometer script will copy all acquisition conguration les to the workstation. 5. Enter the root password for the acquisition system. 6. The acquisition system conguration les on the acquisition system will now be copied to the workstation. 7. rlogin root@eclipse2 to login to the acquisition system computer. 8. uname -r, to list the version of IRIX. 9. For Irix 5.3 go to step B, for Irix 4.0.5 go to step C B. For SGI IRIX v5.3 Indy based systems, follow this procedure: 1. /etc/init.d/local stop to stop the eclipse and control software programs. 2. inst -f eclipse1:/usr/delta/eclipse/dist to start the install
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software and use the Delta workstation directory /usr/delta/eclipse/dist as the distribution directory. This uses the default account guest on eclipse1 to access the directory. 3. go to start the software install process. The system will now install the updated versions of acquisition control programs and conguration les. Note: If a network error or login error occurs then quit, and try step 2. again using the command inst -f root@eclipse1:/usr/delta/eclipse/ dist. 4. quit to exit the install software. 5. init 6 to reboot the acquisition system. The spectrometer will reboot and start the Delta control process for IRIX V5.3. C. For SGI IRIX v4.0.5, V35 based systems follow the following procedure: Note: Delta V3.2 will communicate with Delta V3.1.2 SGI V35 IRIX 4.0.5 based acquisition systems. If you are upgrading from a version prior to V3.1.2 plase upgrade the acquisition system to Delta V3.1.2.
Note: Delta V3.1 is the last version of Delta that will support the SGI 4.0.5 Acquisitions systems. SGI IRIX 4.0.5 has signicant Y2K problems with February 29, 2000, please contact JEOL for more information. 1. killall eclipse control to stop the eclipse and control software programs. 2. exit to return to the workstation. 3. cd /usr/delta/eclipse to change to the eclipse software directory on the workstation. 4. ./update_spectrometer eclipse2, this script will ask for the acquisition system root password twice. 5. Enter the root password for the acquisition system to upload the acquisition system conguration les. 6. Enter the root password for the acquisition system to copy the updated conguration les back to the acquisition system. The new programs for the acquisition system will also be copied to the acquisition system. 7. rlogin root@eclipse2 to login to the acquisition system computer. 8. init 6 to reboot the acquisition system. The spectrometer will reboot and start the Delta control process for IRIX V4.0.5.
V. INSTALLING OR UPGRADING THE DELTA SOFTWARE ON INTEL LINUX OR SUN SOLARIS SYSTEMS
1. Login to the system(root) account. 2. Insert the Delta Software CDROM into the CDROM drive. 3. When the CD disk browser opens click on install_delta to start the Delta install script. 4. Type a letter or number to change the install defaults as appropriate for your system.
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VI. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System from Linux, or Solaris.
5. Type P to proceed with the installation Note: The Delta (Network License) software will not work with Delta (Nodelock License) keys. 6. When the installation is nished close the terminal window if it does not close automatically. 7. To eject the CDROM on Intel Linux systems close the browser window, right click on the CDROM icon and select eject. To eject the CDROM on Sun Solaris systems select Eject from the File menu on the browser window. 8. Put the CDROM in a safe place for future use. 9. Follow the instructions included with the Delta License Key to install the Delta License key, if one is not already installed. 10. If you have an Eclipse+, Eclipse, or Acquisition System attached to your system, continue with section VI Upgrading an Eclipse+, Eclipse or Delta-Upgrade Acquisition System.
VI. UPGRADING AN ECLIPSE+, ECLIPSE, OR DELTA-UPGRADE ACQUISITION SYSTEM FROM LINUX, OR SOLARIS.
1. Login to the system (root) account. 2. Insert the Delta Software CDROM into the CDROM drive. 3. When the CD disk browser opens click on spectrometer_install to start the Delta acquisition software install script. 4. Answer the questions as appropriate for your system. 5. Execute the requested command on the acquisition system. Typically "cd /var/ tmp; sh eclipse.shar". 6. Reboot the acquisition system by typing reboot and answer Y if necessary. 7. The acquisition system will automatically log the user out of the system as the system reboots. 8. Close the terminal if it does not close automatically. 9. To eject the CDROM on Intel Linux systems close the browser window, right click on the CDROM icon and select eject. To eject the CDROM on Sun Solaris systems select Eject from the File menu on the browser window. 10. Put the CDROM in a safe place for future use. 11. When the spectrometer reboot completes the spectrometer is ready for use.
VII. INSTALLING OR UPGRADING THE DELTA SOFTWARE ON IBM AIX SYSTEMS

Login to the system(root) account. Insert the Delta Software CDROM into the CDROM drive. Open a terminal window. Type mkdir /cdrom, to create a directory for the CDROM. Note: Ignore any messages about the directory already being present. 5. Type mount -0 ro -v cdrfs /dev/dco /cdrom to mount the CDROM drive. 1. 2. 3. 4.
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6. Type /cdrom/install_delta to start the install script. 7. Type a letter or number to change the install defaults as appropriate for your system. 8. Type P to proceed with the installation Note: The Delta (Network License) software will not work with Delta (Nodelock License) keys. 9. Type umount /cdrom to unmount the CDROM drive. 10. To eject the CDROM press the eject button on the CDROM drive. 11. Put the CDROM in a safe place for future use. 12. Follow the instructions included with the Delta License Key to install the Delta License key, if one is not already installed. 13. If you have an Eclipse+, Eclipse, or Acquisition System attached to your system, continue with section VIII Upgrading an Eclipse+, Eclipse or Delta-Upgrade Acquisition System.
VIII. UPGRADING AN ECLIPSE+, ECLIPSE, OR DELTA-UPGRADE ACQUISITION SYSTEM FROM AIX.

1. 2. 3. 4. Login to the system (root) account. Create a terminal window. Insert the Delta Software CDROM into the CDROM drive. Mount the CDROM on AIX systems with mount -0 ro- v cdrfs /dev/dco /cdrom . 5. Type /cdrom/spectrometer_install to start the spectrometer install script. 6. Answer the questions as appropriate for your system. 7. Execute the requested command on the acquisition system if necessary. Typically "cd /var/tmp; sh eclipse.shar". 8. Reboot the acquisition system by typing reboot and answer Y if necessary. 9. The acquisition system will automatically log the user out of the system as the system reboots. 10. Close the terminal if it does not close automatically. 11. Type umount /cdrom to unmount the CDROM drive. 12. To eject the CDROM press the eject button on the CDROM drive. 13. Put the CDROM in a safe place for future use. 14. When the spectrometer reboot completes the spectrometer is ready for use.
IX. USER ACCOUNT SETUP

1. Login to the system (root) account. 2. Create a user account with the name delta using the system management tools for the workstation. This is typically /usr/people/delta/. This account is where the user runs Delta, and where the user's raw data, Delta NMR data, and program sources are kept. Select the tcsh for user shell if available. This shell provides command line editing, a history of commands, command completion and many other convenient user features. 3. Create a terminal window.
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IX. USER Account Setup
4. Type login delta to log in to the account created for Delta from a terminal window, and create a terminal window. 5. Type /usr/delta/setup/copy_setup will copy several les to the local directory to allow Delta to be run. Caution: this will copy the following les to *.O versions and copy new les to the directory: .auxchestrc, .chsrc, .grosview, .login, .icons/login.icon, .delta_configure and .delta_parameter_list 6. Logout of the workstation completely. 7. Login to the account created for Delta. 8. Create a terminal window. 9. Type delta -v -n in the terminal window. This should print out the version information for Delta. 10. Delta is now ready to use. Type delta in a terminal window to start the Delta NMR software program. Note: some operating systems may have a menu or desktop icon to start Delta in addition to the command line.
Note: For SGI systems on the Toolchest under Desktop/Customize/

Windows set Save Windows & Desks: to Explicitly, click Set Home Session, and click Close. This will prevent multiple copies of Delta starting if the user logs out of the workstation with Delta running and Save Windows & Desks: set to Continuously.
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APPENDIX M: X WINDOWS EMULATION

X emulation is a process that initiates a Server-Client relationship between the PC/Mac and the Silicon Graphics workstation over a local area network (LAN). SGI IRIX setup: The SGI workstation needs to have the X Display Manager (xdm) active. To determine if xdm is active, open a UNIX shell on the SGI and type chkcong. There should be an entry xdm with a value on or off. If it is off, follow the procedure outlined below. login root chkcong xdm on init 6 Supply the root password. This will turn xdm on. Restart the workstation
X-Server Requirements for PC or MAC:
System Memory Video Memory Screen Resolution Network Input or Keyboard map le
64Mb Minimum 8Mb Minimum 1024x768 TCP/IP Supplied by JEOL (see below). These are located in the /usr/delta/setup/ directory on the SGI workstation. Congure for XDMCP-query, this requires specifying the name or IP address for the SGI workstation. Use the defaults that are standard with the software package. Single window mode. True color representation. 100, 75 and Misc. DPI fonts. The fonts should appear in this order for the best results.
Communication
Protocol Screen Denition: Video Characteristics: Fonts
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PC X-Servers: Exceed by Hummingbird Communications, www.hummingbird.com: After installing the software, place exceed_delta.kbf le in the user directory under the Exceed program directory. Using the conguration tool select exceed_delta.kbf as the default keyboard map. Reections by WRQ Inc., www.wrq.com: After installing the software, place wrq_delta.kbf le in the user directory under the reections program directory. Using the conguration tool select wrq_delta.kmp as the default keyboard. MAC X-Servers: Exodus by White Pine Software Inc., www.wpine.com: After installing the software, place exodus_delta.bin in the Extras directory. Using the conguration tool in Exodus select exodus_delta.bin as the default keyboard. Notes: The X-windows mode of operation with Delta only works with the node locked Delta license. Multiple users on an SGI workstation will impact the overall performance. Up to 3 users on an SGO O2, 180SC, 128 MB system can be supported for 1D and small 2D work. Delta can run on a large SGI server; for example, Challenge-L or Origin 2000. The X-Windows performance is most strongly determined by the PC or MAC and the graphics card used for display.
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Index
Numerics 1 files E-7 1D Processor 5-2, 5-4, I-6 Extended Mode 5-6 Simple Mode 5-3 1D Processor Tool 5-3 1D slice 7-9, 9-7 1d.delta_parameters E-40 2D Data Data Reduction 7-23 Display Modes 7-14 Integration 7-27 Loading 7-1 Mesh Mode 7-14 Panning 7-21 Peak Grouping 7-25 Phasing 7-10 Plotting 7-30 Stack Mode 7-14 Surface Mode 7-14 Zooming 7-21 2D Phasing Tool 7-10 2D Processor 7-3 2D Viewer 7-13 Overview Area 7-21 Projection Area 7-22 Slice Area 7-22 window 7-17 2d.delta_parameters E-44 3D Data Panning 9-18 Zooming 9-18 3D Data Viewer 9-8 3D Slicer 9-12 3d.delta_parameters E-44 A Abs Intgrl 4-45 accelerator keys 1-2, 2-5, 3-3 Acquisition Auto-Place E-34 Experiment Section 10-26 Macro 10-47 Multiple Buffers 10-40
Parameters 4-30 active window 2-3 ADC E-48 ADC_PIPELINE_DEPTH E-48 AIX L-2 All Overlays E-23 Allow Author Login E-33 Allow Connect E-36 ALLOW_MONITOR E-48 ALLOW_OWNED E-49 Amplifier Power Settings 10-42 Annotation 5-55, 7-27, E-23 Rotating 7-29 Shifting 7-29 aqp_program E-64 AQP3_VERSION E-49 Arrayed Parameters 8-1, 10-48 assignment groups E-8 residues E-8 types E-8 Atom Numbers E-29 Select Numbers E-29 Sequence E-29 Attenuators 10-46 Audio filter 10-25 Author E-18 Auto Console E-34 Auto Directory Submit E-33 Auto Level Tool E-34 Auto Process 5-9 Auto Reference 5-35 AUTOGAIN_LOWER E-49 autolock 4-19 Automation 4-1, I-4 Advanced E-36 Lock E-42 Console 4-38 customizing 4-41 E-Mail File E-33 file 4-39 Gradient Shim E-43 Gradient Shim Allowed E-43 multi-user 4-43 Temp. Lock E-42, E-44
Delta Users Guide, v3.2
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templates 4-40 Automation Editor 4-1, 4-35, 4-39, 4-42, F1, F-9 Automation Queue 4-1, 4-35, 4-36, 4-37 Automation Queue Window 4-37 automation templates F-1 Automation Tool 4-34 Auto-phasing 5-30 Autosample Changer slot 10-19 autoshim 4-20 autoshim status 4-19 auxchestrc E-14 Axial Units 5-33 B backup_spectrometer E-16 Balloon Help E-18 Delay E-18 Time E-19 Base_correct 5-14 baseline correction 5-30 BBUS_INTERFACE E-49 Bell Sound E-33 Bias slider 7-19 Black and White Icons E-33 blink.cof E-67 Border E-28 Button Press Freq. E-19 C Calculations 10-36 Audio Filter Delays 10-37 Pulse Angles 10-36 Pulse Widths 10-36 Center E-28 CHANGER E-49 CHANGER_MAX_CHANGE_TIME 49 CHANGER_TIMEOUT E-49 CHANGER_VERSION E-49 chemical shift reference 4-13 COLLECTED_SOUND E-50 Collection Mode 10-43 color background E-32
E-
datazone E-32 foreground E-32 highlight E-32 mode E-33 PM Unselected Color E-32 printer E-22 selected E-32 comment E-23 config_modem.sh E-64 Configuration Editor 1-2 Configuration Files E-17 Confirm window 3-6 Confirmation E-19 CONNECT_DEVICES E-50 Connected Objects 6-11 Connection Tool 3-5, 6-11 Init E-36 Console 4-38, E-3 Color E-34 Coloring E-34 Cut & Paste E-34 History E-35 Wrap E-35 Console Log File E-33 console mode 4-7 Contour E-24 contour line Check E-24 limit E-24 Contour-line level button 7-19 control_aqp2, control_aqp3 E-64 convert E-8 -o switch E-8 convert NMR Data E-8 Copy References Tool 5-36 copy_setup E-14, E-15 COSY Peak J Width E-35 count E-67 Coupling Constants 5-46 CPU performance 3-1 Cryogen cryogen.log file E-66 cryogen level 4-10 cshrc E-14 Current parameter value 10-10
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Cursor I-4 Reference 5-34 cursor E-24 operation 5-20 pick 6-15, 9-16 Cursor Mode 5-20, E-28 Cursor Tool 5-19, 5-20, 5-22, 5-36, 9-15, E-28 Open E-28 Cursor Tool Tab 5-20 D Data E-19, E-24 uploading 4-5 Data Color Slot n Imaginary * E-32 Slot n Real * E-32 Data Display Contour Display 7-17 Datadex Mode 7-15 Data Geometry options menu 6-13 Data Page 3-12 data points 10-28, E-24 Data Reduction 7-23, 9-18 Data Set Active 6-5 Connected 6-11 connecting 3-5 Multiple 6-3 Presentation Control 6-12 Data Slate 3-4, 6-1 3D 9-8 Advanced Operations 6-15 Connect All E-37 Connect Features E-37 Connect X E-37 Expansion 6-17 Horizontal View 6-3 Plot Parameters E-37 Plot Process List E-37 Save Plot Parameters E-37 Slicing 6-15 Vertical View 6-3 Data Viewer 3-4 Datadex Mode 7-15 Date Format E-36
DC Balance 5-13 dead_time 10-37 Debugger I-3 Deconvolve E-24 Sum E-24 Unselected E-24 Decoupler Sequences D-2 Decoupling 10-34, 10-35, 10-42, 10-46, 10-48, D-1 Bilevel 1H D-2 Proton D-1 Deleting Queue Items 4-23 delta 3-1, E-1, E-3 experiments directory E-1 instrument directory E-1 library directory E-1 p_files directory E-1 process_lists directory E-1 reports directory E-2 templates directory E-1 Delta Configuration Files E-17 Delta Console 3-1, 3-2 Accelerator keys 3-3 Menu Bar 3-3 User menu 3-3 Delta Console Preferences Tool E-17 Delta Console window 2-4 Delta Software Installation L-1 Delta Upgrade Spectrometer D-1 Delta.icon E-2, E-14 delta_automation.auto 4-35 delta_automation.auto_automation E-13 delta_configure 3-9, 4-5, 4-25, E-1, E-14, E-15, E-17 .delta_configure_root E-15 delta_drop E-14 delta_parameter_list E-14 delta_product_key E-3, E-6, E-11 delta_screen.rgb E-11 Dependency Graph window 4-40 Dept/Inept I-3 dept_automation 4-42 dept_filter 4-42 dimension features 10-6 ding.aifc E-12 directory tool 3-10
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domain X E-62 Domains 7-4, 9-2, 10-27, 10-35 Active 7-4, 9-3 dot files auxchestrc E-14 cshrc E-14 delta_automation.auto E-13 delta_configure 1-2, 3-2, E-17 delta_configure_root E-15 delta_parameter_list E-14 delta_product_key E-3 grosview E-14 login E-15 Double Click Rate E-19 download E-67 Drag Delay E-19 Draw Backface E-24 Blend E-24 Dither E-25 Double Side E-25 Gradation E-25 Smooth E-25 Solid E-25 Texture E-25 E eclipse 1-1, E-60, E-65 /eclipse Configuration Files E-46 /eclipse Program Files E-64 /eclipse/probes E-60 /eclipse/shapes E-63 Eclipse NMR spectrometer 1-1, 4-1 directories E-1 Edit 4-40 Edit Sample Window 4-40 Editor E-18 Enable E-28 end domain E-62 entropy functional 5-18 eps files E-13 etc/init.d E-68 Ethernet traffic 4-4 exceed_delta.kbf E-15, M-2 Executable E-19 exodus_delta.bin E-15 Expansion 6-17
Experiment 4-1, 4-8, E-19, F-4 Compiling 10-48 Definition 10-1 Error messages 10-48 Header Section 4-26 Instrument Section 4-29 Loading 4-26, 10-2 Macros 10-43 Operators 10-7 Parameters 10-10 Phase Tables 10-38 Pulse Section 4-31 Section 4-40 Selection 4-25 Sequential Execution 4-42 Syntax 10-7 Total Time 10-38 Experiment files 4-26 Experiment Tool 4-1, 4-24, 10-4 Hints E-37 Extended Mode Icons 5-10 F Fast Fourier Transform 5-18 FFT 5-13, 5-18 FG_CONTROLLABLE E-50 FID 4-44, 5-2, 5-3 Audio E-33 FIELD E-50 File E-25 Name E-25 File Manager 3-4, 3-15 Delete Dir Update E-38 Delete Whole Dir E-37 Require Ack Update E-38 Require Acknowledge E-38 Show Errors E-38 Show Errors Update E-38 Show Hidden Files E-38 files E-2 ./files/data E-2 ./files/foreign_data E-2 FILTER_LIMIT E-50 fixup E-10 Font conventions 1-1 Foreign Data E-20 Format Converters E-8
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Freeze Slot E-28 Frequency Offset 10-46 G gamma.def E-46 Gate Assignments 10-45 Geom Border E-25 Geom Tools E-35 Tracking E-35 Geom Windows E-28 Geometry Hints E-27 Negative Contour Grey E-23 Persistent Mode E-27 Rotation E-28 Geometry Page 3-13 get_spectrometers E-15 gif Files E-13 Global E-20 Data E-20 Executable E-21 Experiment E-21 Foreign Data E-21 Instrument E-21 Library E-21 Process List E-21 Report Output E-21 Source E-21 Template E-21 global.rgb E-11 global_percival_operator_library.1 E-7 gr_osview 2-8 Gradient E-50 Gradient Shimming 4-19 Grid E-25 grosview E-14 Group 4-42 Section 4-40, F-3 GSX_AUTOLOCK_TRANS E-50 GSX_COMPAT E-50 GUI 2-1, 2-2 gx filename E-8 gxscon.scn E-65 gyromagnetic ratio 4-13 H Hamming 5-13
handles 2-6 Header Flags 4-26, 10-19 Adding 10-23 Header Parameters 10-10, 10-22 Adding 10-23 Header Section 10-17 Help 3-5, 3-6 HOLD_DELAY E-50 html Files E-13 hw_debug E-67 I iBase_Correct window 5-30 IBM L-2 icons E-2 ident_sipp E-67 IDLE_LOCK E-50 Include Files System 10-16 User 10-16 input file filter 5-4 input focus 2-3 INST_TYPE E-51 Instrument E-18, E-20 Instrument Parameters 4-29, B-1 Adding 10-26 Instrument Section 10-23 integral E-25 2D 7-27 normal E-25 Precision E-25 search width E-35 Tails E-26 Value E-26 Integrals 5-39 Slope adjustment 5-48 Integration 5-36, 5-50 Manual 5-47 Intel L-1 Interactive E-29 interrupt.cof E-67 interrupt_test E-67 IRIX L-1 irr_code 10-34, 10-47, C-1, E-62 Irradiation Codes C-1 Irradiation Modulation 10-47
Index-v
J jdc E-5 JEOL AutoTune probes K-1 JEOL Delta Compiler, jdc E-5 jeol.eps E-11 K kermit-C E-15 Keyboard commands 5-20 Keystroke conventions 1-2 L LC-NMR measurement tool 4-35 Level Tool 5-59, 7-17 Pop E-35 window 7-18, 7-19 LG_SHIMS E-51 library E-20 Line Editor I-4 Line Hiding E-26 Linux L-1 list_header E-11 local E-68 local.rgb E-11 lock channel circuits 4-19 control 4-10, 4-18 signal level monitoring 4-20 solvent 4-10 selection 4-12 status 4-19 lock channel circuits 4-19 Lock Level Meter 4-10, 4-17 lock solvent 4-10 LOCK_TIMEOUT E-51 login 2-1, E-15 login.icon E-2, E-15 Logout 2-9 LOW_HE E-51 LOW_N2 E-51 M machine .alarms E-65 .authorization E-66 .connect E-59 .defaults E-59
.idle_lock E-59 .log E-66 .old E-66 .post_exp E-60 .pre_exp E-59 machine.config 4-5, E-46, E-48 machine.info 4-3, E-56 machine.lg_shims E-56 machine.mx_shims E-56 machine.poll_speeds E-56 MACHINE_LOG E-51 MachinePhase 5-30 macro redefining 5-13 Macros 10-43 Acquisition 10-47 magnetic field strength 4-9, 4-13 make_copy E-66 Max Peaks Allowed E-26 MAX_FG_PULSE E-51 MAX_FILTER_POINTS E-52 MAX_POINTS E-52 MAX_PULSE E-52 MAX_SCANS E-52 Maximum Entropy 5-18 Menu 3-3 method buttons 4-36 file 4-35 section 4-40, F-2 MINIMUM_LOCK_STRENGTH E-52 Miscellaneous Page 3-14 mod return parameter 4-44 module_config 10-41, 10-47 Molecule Borders E-29 Titles E-29 Windows E-29 Mouse Cursor Tool integration operations 5-46 MR spectra 5-18 multi_file Option 10-48 Multiple Buffer Acquisition 10-40 N nD Processor Tool 7-1
Index-vi
nD Processor Tool 7-1 Negative Levels E-31 On E-27 NMR data 3-1 NMR processing 1-1 No Auto Contour E-29 No Zooming E-29 node 4-2 node names 4-2, 4-7 Noise Modulation 10-46 Gating 10-42 NOT_COLLECTED_SOUND E-52 nsend_message E-6 O obs1, obs2, irr1, irr2, tri, qua E-52 offset 4-20 Open Experiment window 4-25 Open File Tool 5-4, 5-6 Open Shim File window 4-16 OPERATION_PROTECT E-52 Operator Cache E-34 Options 6-13 OSC_1H E-52 Overlay Offset X E-29 Overlay Offset Y E-30 Overview 7-21, E-30 P p Files E-5, E-16 page size E-22 Panning 7-21, 9-18 parameter 3-5, 4-43 location E-22 parameters 3-5 Password E-18 paste 3-5 PC X-Servers M-2 peak E-26 Above E-26 Color n * E-32 integral E-22, E-26 Threshold On E-30 Peak Deconvolution 5-51 Peak Display 5-45 Peak Grouping 7-25
peak intensities 8-7 Peak mode deleting peaks 5-37 Peak Pick 5-41, 7-23, 9-18 Peak Picking 5-36 Automatic 5-39 peak position 5-35 performance monitor 2-8 Personal Page 3-7, E-18 Perspective E-30 PGX-300 10-44 phase 4-20 manual 5-27 phase correction 5-28 Phase Sets Addition 10-39 Concatenation 10-39 Phase Tables 10-38 phase_automation 4-42 Phases 90 degree 10-40 Phasing Pivot Point 5-29 phasing 2D Data 7-10 ping 4-7 PiP Font Factor E-30 PiP mode 5-25 plot All Text E-30 Plot Border E-23 Plot Dialog E-23 Plot Options E-22 Plot Tool 5-68 Plot Transparent E-26 Plotting 7-30 PM Center Y-Scale E-38 Font Size E-39 Plot Process List E-39 Template E-20 pmt files E-13 pmt_presentation mgr E-13 Positive Levels E-27, E-31 PP 5-29
Index-vii
PPM 5-14 pps _ presentation mgr E-13 Preferences Tool 3-1, 3-7, 3-10, 4-5 changing parameters 3-10 search window 3-10 Prescans 10-29 Presentation F-4 Presentation Manager 3-4 Operator G-1 Presentation statement F-7 Presentation window 4-40 Preserve Position E-35 PRESERVE_DIALS E-53 Preset button 7-19 Prettify 5-25 print JEOL logo E-22 Printer E-22 Orientation E-22 Paper Size E-22 Tessellate E-22 probe E-62 Probe Attributes 10-33 Probe Codes 10-32 probe file 10-32 Probe Tuning K-3 Values 10-35 Probe Variables 10-36 probe_coarse E-63 PROBE_DELAY E-53 probe_match E-63 probe_tune E-62 Process 1D Macro Definition E-40 Macro Order E-40 Plot Parameters E-40 Plot Process List E-40 Save Auto Apply E-40 Save FID E-41 Save Macro Def E-41 Save Macros E-41 Save Plot Param E-41 Save Simple Mode E-41 Save Timing E-41 Save Tools E-41 Show FID E-40
Show Macros E-40 Show Timing E-41 Show Tools E-41 Simple Mode E-41 View Precision E-40 process command line 4-28 Process FID E-30 Process nD Plot Process List E-42 Process_Global 4-29 Process_Interactive 4-29 Process_Interactive_Global 4-29 Process_Interactive_Local 4-29 Process_Local 4-29 Process_ndimensional 4-29 processing history 3-5 Processing List 5-7 Display functions 5-26 PreTransform 5-14 Transform functions 5-17 Window functions 5-17 processing list 10-18, E-20, E-37 3D 9-3 pulcon.pul E-66 pull E-15 pulse 90s 10-33 90 pulses E-62 Pulse Parameters 10-13 Pulse Programs 10-44 Pulse Section 10-29 pulse viewer 4-32 PULSER_TICK E-53 Q queue 4-8, E-57 .log E-66 .old E-67 Queue Control States 4-21 Queue Modes 4-21 queue.hours E-57 queue.priorities 4-21, E-58 QUEUE_LOG E-53 R Real Time 4-8, 4-44 Real Time monitor display 4-8
Index-viii
receiver gain 10-24 Reference 5-35, I-3 Reference Command 5-35 reference registers 5-35 Reference Tool 5-34 reference value 5-35 Referencing 5-34, 7-23 Region Manipulation E-30 Region mode 5-24 regions E-26 Relaxation Data 8-1 Calculation 8-3 Collection 8-1 Processing 8-2 relaxation delay 4-44, 10-30 Relaxation Times 8-3 Report Output E-20 restore_spectrometer E-16 Resulting File window 6-11 RF filters 4-20 RF Phase 10-46 RF_SHAPER E-53 S sample 4-7, 4-10, F-1 changer 4-10, 4-23 loading 4-1, 4-7, 4-10 spinning 4-10, 4-11 state 4-10 temperature control 4-12 Sample Control Tool 4-9, 4-43 Gradient Shim E-39 Verify E-39 sample ID 4-21 sample name 4-21 SAMPLE statement F-1 Sample Status 4-36 SAMPLE_DELAY E-53 SAMPLE_SOUND E-53 Save Color & Font E-35 Save Data File window 5-67 Save Shim File window 4-16 Saving Processed Data 5-6 sawth 4-1 window 4-43 Sawtooth 4-43 Lock Signal Display 4-43
SAWTOOTH_SHIFT E-53 SAWTOOTH_TRIM E-54 Scale Solvent E-27 scans 10-28 Send_data_to_finger 4-29 send_message E-5 sequence marker E-27 Set process window 4-27 SGI L-1 Shadow Dimensions E-27 shim control 4-10 Shim Files 4-15 Shim Tool 4-13 Controls 4-14 Nomenclature 4-14 shim values 4-20 SHIM_KNOB BOX E-54 shims 4-10 loading from data files 4-10 spinning and nonspinning 4-14 Show Deconvolution E-36 Show Peak Count E-36 Show Tools 5-3 Silicon Graphics user interface 2-1 Simple Mode E-19 Processor Buttons 5-79 Single Buffering E-34 Single Exponential 5-17 Site E-18 slice slicing 6-15 Solaris L-2 solvent 10-24 solvent.def 4-19, E-58 SOUND_DURATION E-54 Source E-20 Spectral Offset 10-27 Spectral Widths 10-28 Spectrometer 4-1 connection 3-5 Load E-34 monitor E-34 monitoring 4-6 selection 4-2 unlinking 4-7
Index-ix
Spectrometer Control Tool 4-1, 4-2, 4-7, 10-2 Double-Click E-39 functions 4-3 Gain 4-19 Locking 4-18 Menus 4-9 queue menu 4-21 Selection 4-2 Solvents 4-18 Tools 4-7 spectrum 5-18 Spin Lock Pulses 10-34 SPIN_GAS_SOURCE E-54 spin_lock_90 E-62 spin_lock_attn E-62 SPIN_SLOP E-54 SPIN_TIMEOUT E-54 spinning_delta#.RGB info E-12 Spread Sheet I-5 Spreadsheet 3-5 Spreadsheet Tool 5-64, 7-30 standard files 4-26 Standard Include Files A-1 Start slider 7-18 Startup Default 5-3 Startup Console E-18 Statements Align 10-14 Assignment 10-8 Collect 10-43 Conditional 10-15 Define 10-12 Loop control 10-15 Macro 10-14 Statistics E-27 std_2d_acquisition A-1 std_3d_acquistion A-2 std_acquisition A-5 std_header 10-17, A-4 std_include 10-17 std_instrument A-5 std_pulse A-5 Stereo E-30 STRICT_SOLVENT E-54
Sun L-2 Supervisor Alert E-43 SUPPRESS_FW_WARNINGS E-54 Sweep Widths 10-28 Sweep/Offset Adjust E-36 swept lock signal display 4-8 SYNC0_BUS_LINE E-54 system Delta directories E-1 System Usage 2-8 T T1 Analysis I-3 T1 Analysis Tool 8-1 TEMP_HOLD E-54 temp_limit_hi E-62 temp_limit_lo E-62 TEMP_SLOP E-55 TEMP_TIMEOUT E-55 Temperature 10-25 control 10-25 Limits 10-34 Parameters 10-25 template E-20 Template File Format G-1 terminal console program H-1 Terminal shell 2-8 test_lights E-68 test_serial_fiber E-68 Time-shared Homonuclear Decoupling 1042 Toggle Slot E-31 Tool Bar 3-3 Tool Bar Icons 3-3 Tool Icons 1D Processor I-6 3D Plotter I-6 Automation I-3, I-4 Automation Editor I-4 Autoqueue I-3 Calculator I-3 Chart I-4 Connect I-4 Connection I-5 Console manager I-2 Cursor I-4 Data slate I-3 Debugger I-3
Index-x
Delta console I-2 Dept/Inept I-3 Experiment tool I-2 Export I-2 File Math I-2 Geometry tool I-2 Get directory I-1 Import I-2 Interactive base correction I-2 Level I-4 Line Editor I-4 nD Processor I-7 Parameter Editor I-4 Parameter tool I-1 Parameter Viewer I-6 Peak List I-6 Phase 2D I-1 Pick tool I-1 Preferences I-5 Presentation Manager I-1 Presentation Manager template I-1 Process I-7 Reference I-3 Signal/Noise I-5 Spectrometer I-5 Spread Sheet I-5 T1 Analysis I-3 Template I-6 Transfer Integral I-5 View Control I-5 Widget Editor I-6 Window Phaser I-6 Toolchest 2-6, 3-1 Tools Experiment 10-5 Tools page E-36 total_time 10-30 Track Position E-31 Transform Function 5-17 Transparent E-31 Transparent X Ruler E-31 Transparent Y Ruler E-31 Transparent Z Ruler E-31 TSC_AVAILABLE E-54 TSC_TIMEOUT E-55
U Unix J-1 Unix Commands J-1 UNIX Shell 2-9 Unlink 4-7 update_spectrometer E-16 Upgrading an Acquisition System AIX L-8 Linux L-7 SGI L-5 Solaris L-7 Upgrading the Delta Software AIX L-7 Linux L-6 SGI L-3 Solaris L-6 upload E-7 UPLOAD_EXPIRE E-55 User Account E-1, E-14 USER Account Setup L-8 USER Setup E-14 User Shims 4-16 usr/delta /usr/delta/eclipse E-16 /usr/delta/eclipse/probes E-16 /usr/delta/source E-16 usr/delta/eclipse/dist E-16 usr/delta/global E-6, E-7, E-11, E-13 Files E-3 usr/delta/global/automation E-13 usr/delta/global/experiments E-13 usr/delta/global/help E-13 usr/delta/global/process_lists E-13 usr/delta/global/templates E-13 usr/delta/global Directories E-13 usr/delta/global/automation E-13 usr/delta/setup E-14 usr/eclipse E-66 usr/eclipse/testprog E-67 V variable temperature 4-10 Vector View Auto Off E-39 Processing E-39 verify E-6 VI Commands J-2
Index-xi
View Control I-5 View Tool 4-1, 4-8, 4-44 View Vector 4-44 virtual geometry 3-2 VTEMP E-56 W widgets 3-1 Window Full screen 2-6 Iconifying 2-5 Menu Button 2-4 Moving 2-6 Resizing 2-6 Structure 2-3 X X Display Manager M-1 X ruler E-31 X Windows Emulation M-1 x_90_width 10-30 xxxx .dials E-63 .limits E-63 .probe E-60, E-62 .shims E-63 .shims.0 E-63 Y Y ruler E-31 Z Z ruler E-31 Zerofill 5-15 Zoom mode 5-23 Zooming 9-18
Index-xii

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Delta NMR Software Users Guide

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

ABOUT THIS GUIDE

BEFORE YOU BEGIN

DELTA Users Guide, v 3.2

DELTA Users Guide, v 3.2

CHAPTER 2: USER INTERFACE BASICS

A password box will appear on the screen.

DELTA Users Guide, v 3.2

Chapter 2: User Interface Basics

DELTA Users Guide, v 3.2

Mouse and Keyboard

MOUSE AND KEYBOARD

DELTA Users Guide, v 3.2

Chapter 2: User Interface Basics

Window Menu Button Path Bar Drop Pocket Pathname Field

Maximize Button Iconize Button

Figure 2-3. Basic IRIX Window Structure

WINDOW MENU BUTTONS

Maximize Alt F10 Raise Lower Close Alt F1 Alt F3

DELTA Users Guide, v 3.2

Iconifying or Minimizing Windows

Figure 2-4. Window Menu Button

ICONIFYING OR MINIMIZING WINDOWS

Minimize (Alt+F8) [or Iconifying]

Maximize (Alt+F10) [or Restore (Alt+F5)]

Figure 2-5. Minimized and Maximized Windows

DELTA Users Guide, v 3.2

Chapter 2: User Interface Basics

MAXIMIZING WINDOWS TO FULL SCREEN

Figure 2-6. Moving and Resizing Windows

DELTA Users Guide, v 3.2

Figure 2-7. Silicon Graphics User Toolchest

Figure 2-8. Selected Menu

DELTA Users Guide, v 3.2

Chapter 2: User Interface Basics

WORKSTATION SYSTEM USAGE

Figure 2-9. System Usage Monitor

DELTA Users Guide, v 3.2

Figure 2-10. Silicon Graphics UNIX Shell Window

Figure 2-11. Silicon Graphics Logout Conrmation Window

DELTA Users Guide, v 3.2

Chapter 2: User Interface Basics

DELTA Users Guide, v 3.2

CHAPTER 3: GETTING STARTED ON DELTA

DELTA Users Guide, v 3.2

Chapter 3: Getting Started On Delta

Note: Extremely large data les can slow down Delta.

THE DELTA CONSOLE