Manual SyByL

Basics Manual
SYBYL®-X 1.1
Early 2010
1699 South Hanley Rd. Phone: +1.314.647.1099

St. Louis, MO Fax: +1.314.647.9241
63144-2917 http://www.tripos.com
LEGAL NOTICE
SYBYL and related Tripos modules © 1991-2010 Tripos, L.P. All Rights Reserved.
Benchware and related Tripos modules © 2005-2010 Tripos, L.P. All Rights Reserved.
AUSPYX © 2001-2010 L.P, Inc. All Rights Reserved.
Almond © 2003-2010 Molecular Discovery Ltd. All Rights Reserved.
AMPAC © 1997-2010 Semichem. All Rights Reserved.
AMM-2001 module in AMPAC version 8.16.5 © 2001 Regents of the University of Minnesota. All Rights Reserved.
Concord, Confort, CombiLibMaker, DiverseSolutions, ProtoPlex and StereoPlex © 1987-2001 University of Texas at
Austin. All Rights Reserved.
FlexX, FlexX-Pharm, FlexE, and FlexS © 1993-2010 BioSolveIT. All Rights Reserved.
FUGUE, JOY, HOMSTRAD, ORCHESTRAR © 2010 Cambridge University Technical Services, Cambridge,
England. All Rights Reserved.
RACHEL © 2002-2010 Drug Design Methodologies.
Surflex, Surflex-Dock, and Surflex-Sim © 1998-2010 BioPharmics LLC. All Rights Reserved.
VolSurf and Almond © 2001-2010 Molecular Discovery Ltd. All Rights Reserved.
Portions copyright 1992-2010 FairCom Corporation. All Rights Reserved.
This material contains confidential and proprietary information of Tripos, L.P. and third parties furnished under the
Tripos Software License Agreement. This material may be copied only as necessary for a Licensee’s internal use
consistent with the Agreement. The allowed use includes printing of hardcopy versions hereof as minimally necessary
for Licensee’s internal use. Neither Tripos, L.P., nor any person acting on its behalf, makes any warranty or
representation, expressed or implied, with respect to the accuracy, completeness, or usefulness of the material
contained in this manual or in the corresponding electronic documentation, nor in the programs or data described
herein. Tripos, L.P. assumes no responsibility nor liability with respect to the use of this manual, any materials
contained herein, or programs described herein, or for any damages resulting from the use of any of the above. Except
for printing of hardcopy versions as stated, no part of this manual may be reproduced in any form or by any means
without permission in writing from Tripos (DE), Inc., 1699 South Hanley Road, St. Louis, Missouri 63144-2917, USA
(314-647-1099).
Selected software programs for methodologies contained or documented herein are covered by one or more of the
following patents: Comparative Molecular Field Analysis (CoMFA): US 5,025,388; US 5,307,287; US 5,751,605; AT
E150883; BE 0592421; CH 0592421; DE 691 25 300 T2; FR 0592421; GB 0592421; IT 0592421; NL 0592421; SE
0592421. HQSAR: US 6,208,942. Embedded NLM: US 6,675,103. Topomers: US 6,185,506; US 6,240,374; US
7,184,893; US 7,212,951. TopCoMFA: US 7,329,222. DBTop: US 7,330,793. OptiSim: US 6,535,819. Surflex
software programs for chemical analysis by morphological similarity: US 6,470,305 B1.
SYBYL, UNITY, CoMFA, CombiFlexX, Concord, DiverseSolutions, GALAHAD, LeapFrog, OptDesign, StereoPlex,
and Alchemy are registered trademarks of Tripos, L.P.
AUSPYX, Benchware, CScore, DISCOtech, Distill, GASP, HQSAR, Legion, MOLCAD, Molecular Spreadsheet,
Muse, OptiDock, OptiSim, Pantheon, ProTable, ProtoPlex, Selector, SiteID, Topomer CoMFA, Topomer Search,
Tuplets, and Tripos Bookshelf are trademarks of Tripos, L.P.
RACHEL is a trademark of Drug Design Methodologies.
Surflex, Surflex-Dock, and Surflex-Sim are trademarks of BioPharmics LLC.
“FairCom” and “c-tree Plus” are trademarks of FairCom Corporation and are registered in the United States and other
countries.
All other trademarks are the sole property of their respective owners.
SYBYL Basics Table of Contents
Chapter 1.
Introduction to SYBYL Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.1 License Requirements for SYBYL Basics . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.2 What is New with SYBYL Basics Features . . . . . . . . . . . . . . . . . . . . . . . 9
Chapter 2.
Quick Introduction to SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.1 Start SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.2 Load Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.3 Rotate, Translate, and Scale Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.4 Save a Molecule to a File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.5 Get Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.6 Exit SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
2.7 Starting SYBYL and Setting its Environment . . . . . . . . . . . . . . . . . . . . . 23
Chapter 3.
The SYBYL Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.1 The SYBYL Menubar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
3.2 The SYBYL Toolbar Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
3.3 The SYBYL Textports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
3.4 Special Keyboard Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Chapter 4.
Open and Save Files of Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
4.1 Open Files via the Menubar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
4.2 Save a Molecule File via the Menubar . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.3 Open/Save Mol2 Files via the Command Line . . . . . . . . . . . . . . . . . . . . 41
4.4 Open and Save in Other Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
4.5 Convert Between Molecular File Formats . . . . . . . . . . . . . . . . . . . . . . . . 44
4.6 View and Edit Text Files in SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Chapter 5.
Understand Molecule and Display Areas . . . . . . . . . . . . . . . . . . . . . . 51
5.1 What are Molecule and Display Areas? . . . . . . . . . . . . . . . . . . . . . . . . . 52
5.2 Change the Default Molecule Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
5.3 Copy Between Molecule Areas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
5.4 Merge Molecule Areas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Chapter 6.
Select Atoms, Bonds, or Substructures . . . . . . . . . . . . . . . . . . . . . . . 61
6.1 Selecting With the Mouse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
6.2 The Selection Menu and Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
SYBYL-X 1.1 SYBYL Basics TOC-3

6.3 General Description of the Expression Dialogs . . . . . . . . . . . . . . . . . . . . 67
6.4 How to Use the Atom Expression Dialog . . . . . . . . . . . . . . . . . . . . . . . . 75
6.5 How to Use the Bond Expression dialog . . . . . . . . . . . . . . . . . . . . . . . . . 82
6.6 How to Use the Substructure Expression Dialog . . . . . . . . . . . . . . . . . . . 85
Chapter 7.
Clear and Reset the SYBYL Display . . . . . . . . . . . . . . . . . . . . . . . . . . .89
7.1 Clear the Screen and Delete Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
7.2 Reset Scaling, Translation, and Rotation . . . . . . . . . . . . . . . . . . . . . . . . . 93
7.3 Undo the Last Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Chapter 8.
Build and Modify Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .95
8.1 Sketch a Small Molecule Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
8.2 Ring Fusion Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
8.3 Load Fragments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
8.4 Access the Sketcher . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
8.5 Modify Molecules Outside of the Sketcher . . . . . . . . . . . . . . . . . . . . . . 118
8.6 Define and Modify Geometric Features . . . . . . . . . . . . . . . . . . . . . . . . 138
Chapter 9.
Geometric Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .147
9.1 Intra-/Intermolecular Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
9.2 List Coordinates, Distances, or Angles . . . . . . . . . . . . . . . . . . . . . . . . . 149
9.3 Measure the Intramolecular Angle Between Planes . . . . . . . . . . . . . . . 150
9.4 Measurements Specific to UNITY Features . . . . . . . . . . . . . . . . . . . . . 151
Chapter 10.
Get Information on SYBYL Objects . . . . . . . . . . . . . . . . . . . . . . . . . .153
10.1 Information on Selected Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
10.2 List Information About SYBYL Objects . . . . . . . . . . . . . . . . . . . . . . . 155
10.3 Print Information About SYBYL Objects . . . . . . . . . . . . . . . . . . . . . . 156
Chapter 11.
Use Molecule Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .157
11.1 Database Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
11.2 Database Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
11.3 Open and Close SYBYL Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
11.4 Retrieve Molecules from a SYBYL Database . . . . . . . . . . . . . . . . . . . 169
11.5 Obtain Information on Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
11.6 Manage Database Content . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
11.7 Save Database Molecules to Mol2 Files . . . . . . . . . . . . . . . . . . . . . . . 178
11.8 Database Qualifiers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
TOC-4 SYBYL Basics SYBYL-X 1.1

11.9 The DATABASE Command . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
11.10 System Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Chapter 12.
Manage SYBYL Sessions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
12.1 Save a SYBYL Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
12.2 Open (Restore) a Saved Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
12.3 Delete a Saved Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
12.4 Open a New Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
12.5 Close a SYBYL Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
12.6 Record and Play Back SYBYL Operations . . . . . . . . . . . . . . . . . . . . . 191
Chapter 13.
SYBYL Objects and Their Expressions . . . . . . . . . . . . . . . . . . . . . . . 197
13.1 Definitions of SYBYL Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
13.2 Formats for Specifying Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
13.3 Create Complex Expressions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
Chapter 14.
Sets in SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
14.1 Global Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
14.2 Local Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
14.3 Dynamic Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
14.4 Built-in Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
14.5 Static Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228
14.6 Working with Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
Chapter 15.
Libraries of Chemical Groups and Fragments . . . . . . . . . . . . . . . . . 231
15.1 Group Library Structure and Contents . . . . . . . . . . . . . . . . . . . . . . . . . 232
15.2 Fragment Library Structure and Contents . . . . . . . . . . . . . . . . . . . . . . 233
Chapter 16.
Advanced SYBYL Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
16.1 Automatic Command Execution at SYBYL Startup . . . . . . . . . . . . . . 238
16.2 Execute a SYBYL Command on Multiple Molecules . . . . . . . . . . . . . 239
16.3 Define Markush Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
SYBYL-X 1.1 SYBYL Basics TOC-5

This page intentionally blank.
Chapter 1.
Introduction to SYBYL Basics
SYBYL uses computer analysis to assist in the description and prediction of

molecular behavior. SYBYL Base includes the basic tools for molecular
modeling. Topics in this manual include:
• Quick Introduction to SYBYL on page 13
• Rotate, Translate, and Scale Molecules on page 17
• The SYBYL Window on page 25
• Open and Save Files of Molecules on page 33
• Understand Molecule and Display Areas on page 51
• Select Atoms, Bonds, or Substructures on page 61
• Clear and Reset the SYBYL Display on page 89
• Build and Modify Molecules on page 95
• Geometric Measurements on page 147
• Get Information on SYBYL Objects on page 153
• Use Molecule Databases on page 157
• Manage SYBYL Sessions on page 183
• SYBYL Objects and Their Expressions on page 197
• Sets in SYBYL on page 215
When combined with SYBYL applications, SYBYL Base provides a completely

integrated environment for computational chemistry and molecular modeling.
SYBYL-X 1.1 SYBYL Basics 7

Chapter 1. Introduction to SYBYL Basics
License Requirements for SYBYL Basics
1.1 License Requirements for SYBYL Basics

Consolidated Licensing
SYBYL-X introduced a simplified licensing scheme in which the “SYBYL”

license provides access to all functionality described in this manual.
Two additional keys perform the following functions:

• SYBYL_Interactive: Controls interactive access to SYBYL and other
programs
• CPU: Allows batch operations
Module-Based Licensing
SYBYL continues to run with a license file issued before the SYBYL-X release.
The functionality described in this manual requires a “SybylBasic” license.
Additionally, a “BioPolymer” license:

• is required to assign and label AMBER and Kollman atom types;
• is used, if present, to add hydrogens to proteins, nucleic acids and
saccharides.
8 SYBYL Basics SYBYL-X 1.1

What is New with SYBYL Basics Features
1.2 What is New with SYBYL Basics Features

New and Modified Functionality
New in SYBYL-X 1.1

Explore the new selection model:
• Select any atom or surface by simply clicking on it. Double-dick an
atom to select the substructure, triple-click to select the entire molecule.
Ctrl-Alt and drag to select atoms in a rectangular area.
• More about Selecting With the Mouse.
• Most functionality has been modified to work on pre-selected atoms or
entire molecule areas. Discover The Selection Menu and Icons.
New toolbars provide easy access to a vast array of display functions without
the need for dialogs, reducing the number of mouse clicks for basic operations.
• Each toolbar may be repositioned and customized.
• Discover The SYBYL Toolbar Icons.
Atom rendering is now part of the molecular description and

no longer a background image. Mix the rendering styles within a molecule to
highlight regions of interest by, for example applying spacefill to the metals and
capped sticks to the ligand. Rendering styles are saved in Mol2 and session
files.
The SYBYL Window

SYBYL-X introduced a new, modern look:
• The command console is now docked into the main window. An
additional message area receives the text output of system operations.
• It is now possible to navigate within the menu and dialogs via keyboard
hot keys and the mouse’s scroll wheel.
• All dialogs may be closed by clicking the X in the corner of their
window.
• The F1 keys launches the Tripos Bookshelf, SYBYL’s online Help.

Expression Dialog Redesign

The various expression dialogs (Atom Expression, Bond Expression, etc.) and
subdialogs have been significantly redesigned. Some of the changes include:
• A hierarchical listing of items that can be expanded and collapsed as
needed. This hierarchy provides easy multi-item selection (e.g., clicking
a substructure name automatically selects all atoms in that substructure).
• A right-click menu in the hierarchy contains options for inverting the
selection within a substructure, within a chain, or within the entire
molecule, where applicable.
• There are partial selection indicators (grey check marks versus bold
check marks) to help you identify when, for example, some but not all
atoms of a substructure are selected.
• Boolean operations on selected sets of items are now accomplished by
defining both sets first and then specifying the Boolean operation.
See the Expression dialog description for more information. [SYBYL-X]
New Look for the SYBYL Sketcher

The SYBYL Sketcher (Edit > Sketch Molecule) is driven by a set of toolbars.
[SYBYL-X]
• Sketcher functions
• Atomic symbols, with access to the full periodic table
• Groups, as defined in the Group Library. Note that a group can only be
added to an existing atom.
Note that, with this new design, loading fragments and changing Tailor settings
(e.g., clean up methods) must now be made before accessing the Sketcher.
The Sketcher operates on different molecule areas depending on atom selection:

• To modify an existing molecule you must select one of its atoms before
invoking the Sketcher.
• To sketch a new molecule, clear all selection then invoke the Sketcher.
The new molecule will be sketched in the first, empty molecule area.
Pseudo-atoms
The ability to define pseudo-atoms is once again available. It places dummy
atoms at the centroid positions of prochiral, methyl, and phenyl ring groups. See
Add Pseudo-atoms (Centroids) on page 119. [8.1]
• Edit > Add > Pseudo-atoms
• ADD_PSEUDOATOMS mol_area

Reading .sd Files

Files with the .sd extension can beloaded directly from the Open File dialog.
[SYBYL-X]
Known Limitations
DATABASE
If your machine is on a network and has only the NFS client operating system
software installed (i.e., not the NFS server software itself), a SYBYL session
running on that machine will fail to open databases residing on NFS mounted
disks connected to a remote machine. When you try to open a database, you will
get a CANT_GET_LOCK error.
Install the NFS server operating system software to fix the problem. This
problem does not occur if your machine is completely stand-alone or if you
have the NFS server operating system software installed.

Chapter 2.
Quick Introduction to SYBYL
Run this tutorial to learn some basics operations in SYBYL:

• Start SYBYL on page 13
• Load Molecules on page 16
• Change the Display on page 16
• Save a Molecule to a File on page 20
• Get Help on page 21
• Exit SYBYL on page 22
• Starting SYBYL and Setting its Environment on page 23
A Matter of Time: This tutorial requires about 5 minutes of personal time.
2.1 Start SYBYL

Windows Users:
¾ Double-click the SYBYL-X 1.1 icon on your desktop or find SYBYL-X
1.1 in your computer’s All Programs list.
Linux Users:
¾ If there is a SYBYL-X 1.1 icon on your desktop, double-click it.
Otherwise open a system shell.
Start the SYBYL program using Trigo:

¾ At the system prompt type: trigo sybylx1.1
SYBYL Session
A SYBYL session begins when you start SYBYL and ends when you close it.
The current state of a SYBYL session can be saved and reloaded at a later time.
You may also run multiple sessions simultaneously. See Manage SYBYL
Sessions on page 183 for more details.

Chapter 2. Quick Introduction to SYBYL
Start SYBYL
Explore the SYBYL Window

The SYBYL graphical interface is composed of a menubar, toolbar icons, a
graphics area, and a text console.
Menubar
A SYBYL menu option can:
• be a simple command: Edit > Delete Everything
• lead to submenus: Biopolymer > Model Proteins > ORCHESTRAR
• open a dialog: File > Import File...
Each list of menu options can be detached from the menubar so that it remains
visible even after a selection is made.
• To detach a menu: click the dashed line above the first item.
• To close a tear-off: click the X in the upper right corner.
When you initiate an operation by clicking a menu item, no other operation is

possible until either that operation completes or you cancel it. All menubars are
greyed out while the current operation is active.

Start SYBYL
Additional Information:
• The SYBYL Menubar on page 26
• Menu, Dialog, and Mouse Shortcuts on page 27
Toolbars
Use the icons in the SYBYL toolbars to interact with the graphics. Clicking
some icons immediately performs an action, others require a selection to be
made from a pull-down, and others display a tool that can remain open as you
work or can be closed by pressing the X button in the corner of its window.
Command Console
Use this console to enter any command at the SYBYL command prompt
(SYBYL>). After entering a command, the system performs the command
operation and redisplays the SYBYL command prompt. See the List of SYBYL
Commands in the Reference Guide.
Note: The menubar and command line are available simultaneously.
System Messages
A few SYBYL operations report information in this area. You may also type
simple system commands in the Command Console (e.g. cmd ls to list the files
in the current directory or folder). The output of such a command appears in the
System Messages area.
See The SYBYL Window on page 25 for more in-depth description or the
SYBYL interface.

Load Molecules
2.2 Load Molecules

Molecules can be loaded into SYBYL from files. A Fragment Library is also
available, containing a number of small, mostly cyclic, molecules.
2.2.1 Load a Molecule from a File:

Read in dicloxacillin from a list of demo files distributed with SYBYL.
¾ File > Import File ( )
¾ In the Open File dialog, click [$TA_DEMO] in the Bookmarks section

on the left.
The contents of SYBYL’s demo directory are displayed in the sections on the
right.
¾ Select example.mdb in the Directory Navigation list in the center.
¾ Select dicloxacillin.mol2 in the Selection list on the right then press

OK.
SYBYL loads dicloxacillin into M1, the default molecule area if you started
with a blank screen. A molecule area is a region of memory that holds a
particular molecule.
2.2.2 Load a Molecule from the Fragment Library:

Load vitamin B2.
¾ File > Get Fragment
¾ Select VITAMIN B2 in the list of available molecules and press OK.
SYBYL loads vitamin B2 into M2, the first empty molecule area.
Both molecules are displayed in the center of the SYBYL window. In the next
section, you will learn how to change the display so that you can see the
molecules more clearly.
2.2.3 Change the Display

1. Change the display so you can see the molecules side-by-side.
¾ Click on the Display toolbar and select Half.

Rotate, Translate, and Scale Molecules
SYBYL displays the molecules in display areas D1 (right) and D2 (left).
For more information, see What are Molecule and Display Areas? on page 52.
2. Toggle the display for each molecule off and on.
¾ Click on the Molecule toolbar.
¾ In Molecule Display Options dialog, for row M1, toggle the check box in
the Mol Vis column off and then on.
Notice also that the check box appearance changes. Watch the SYBYL screen
when you toggle the display off and on. Likewise, the other molecule can be
displayed and undisplayed using the respective check box.
¾ Display both molecules and click the X in the upper corner to close
the dialog.
2.3 Rotate, Translate, and Scale Molecules

Structure rotation is based on the Cartesian coordinate system such that the
X-axis is horizontal, the Y-axis is vertical, and the Z-axis is perpendicular to the
viewer.
SYBYL supports a three-button mouse, reserving the right button for context
sensitive menus. When using a touch pad use on the Mouse Mode toolbar.
2.3.1 Move All Objects Together
Move All Objects Mouse Keyboard

X,Y rotation Left
X,Y translation Middle —
Left Shift
Z rotation Left Ctrl+Shift
Z translation Middle Ctrl
90° rotationa — Ctrl+arrow keys
a. To change the rotation increment from its default of 90°:
TAILOR SET GRAPHICS KEYBOARD_ARROW_ROTATION.
Linux Usage Note

If the Ctrl or Alt keys do not behave as described above it may be because of a
preference setting for your window manager. We recommend the following
setting for the Gnome window manager:

• System (or Applications) > Preference > Windows

• Set Movement Key to Super (or “Windows logo”).
1. Rotate both molecules. When you start a SYBYL session all images on the
screen are affected simultaneously by rotations and translations.
¾ With the cursor in the graphics window, press the left mouse button
and move your mouse in any direction.
Notice that all molecules move. This is because your current mouse focus
setting is G (global), as indicated by the icon on the Mouse Mode
toolbar.
2. Rotate the molecules about the Z-axis.

¾ Simultaneously hold down the Ctrl and Shift keys while pressing
the left button and dragging left or right.
2.3.2 Move Selected Objects Only

To move one or more, but not all, objects simultaneously you must first select
them. Then add Alt to the key/mouse combination:
Move Selected Objects Mouse Keyboard

X,Y rotation Left Alt
X,Y translation Middle Alt
Left Alt+Shift
Z rotation Left Alt+Ctrl+Shift
Z translation Rotate all objects in X,Y by 90°
then select the object(s) of interest
and translate them in the XY plane.
3. Move dicloxacillin to the upper right corner.

¾ Click an atom in dicloxacillin.
¾ Hold down the Alt and Shift keys while pressing the left button and
dragging the cursor to the upper right corner of the display area.
Vitamin B2 remains stationary.
An alternative method is to change the mouse focus using a toolbar icon.
¾ Clear the selection first by clicking on the Selection toolbar.

¾ Click on the Mouse Mode toolbar.
SYBYL opens the Mouse Focus Options dialog with a list of molecules.
¾ Click M1 dicloxacillin.
SYBYL changes the mouse focus to M1. Note that the notation on the icon
changed from G to M1. This notation represents the active object for the
mouse focus.
¾ Middle-click and drag dicloxacillin to the lower right corner.

If you had multiple molecules in D1, all of those molecules would move
together. In such cases, to only move a particular molecule using this dialog,
click the name of the molecule in the list, then use the mouse.
4. Move vitamin B2 to the upper left corner.

¾ In the dialog click M2 vitamin B2.
SYBYL changes the mouse focus to M2 only.
¾ Middle-click and drag vitamin B2 to the upper left corner.
¾ Reset the mouse focus to Global then click X in the upper corner to
close the Mouse Focus Options dialog.
2.3.3 Zoom Objects with the Mouse

The zoom modifies the scale of all objects, whether visible or not.
Mouse Zooming Action

Wheel Scroll forward to zoom in by 5%.
Scroll backward to zoom out by 5%.
Left+Middle Drag the mouse to the upper right to zoom in.
or Ctrl+Left Drag the mouse to the lower left to zoom out.
5. Modify the size of the molecules.
¾ Use the mouse’s scroll wheel to increase the size of both molecules.
If your mouse does not have a scroll wheel use either of the alternatives
described above.

Save a Molecule to a File
2.3.4 Reset Rotation, Translation, and Scale

All rotations, translations, and scale operations applied globally or individually
can be reset with a single click.
¾ Click .
2.3.5 Moving Objects in a Single Display Area

If you have four or fewer molecules in different display areas and you want to
manipulate one of them independently of the others you can toggle the mouse
focus between Global (all together) and a single one by pressing a function key.
The label of the Mouse Focus icon ( ) will reflect the current status.
• F9—toggles between Global and D1
• F10—toggles between G and D2
¾ Experiment with function keys F9 and F10 to move each molecule
independently of the other, then both together.
¾ Be sure to toggle the function keys back to Global when you are
done.
2.4 Save a Molecule to a File

¾ File > Export File ( )
SYBYL opens the Save Molecule dialog.
¾ Verify that m1: dicloxacillin is highlighted in the list; if not, select it.
¾ Type diclox_tut in the File field.
¾ Press Save.
SYBYL creates a file named diclox_tut.mol2 in your current directory.
Note: You can select multiple structures and save them in a specified format.
For more information, see Save a Molecule File via the Menubar on page 39.

Get Help
2.5 Get Help

To learn about a specific feature or dialog:
• Press the keyboard F1 key.
• Press the Help button in any dialog.
• Select Help on the SYBYL menubar.
• Type HELP in the console.
The Tripos Bookshelf is SYBYL’s complete online documentation. It is

organized by SYBYL application and consists of:
• HTML-style pages that provide context-sensitive help within the
software. To ensure easy navigation, each page is linked to the table of
contents and the index of the book it belongs to as well as to the Tripos
Bookshelf’s main page. It is also equipped with a bread crumb locator.
• PDF copies of all the manuals. The “View or Print” link in each
Bookshelf topic’s main page gives you access to the complete documen-
tation for that topic in PDF format.
• A full text search engine.
2.5.1 Search for Specific Information

To use the search engine click the Search tab then type the text you want to
look for in the search box and click Search or press the Enter key on your
keyboard. The list of documents found is ordered by decreasing number of
occurrences of the search text.
To access the documentation independently of the SYBYL application, direct

your favorite web browser to TriposBookshelf/index.html within your
SYBYL installation.
2.5.2 SYBYL Version and Local System Information

Help > About SYBYL
A dialog provides the following information:

• The SYBYL version, platform type, and creation date.
• The copyright notice.
• Your Server Host ID number. After registering to the Tripos Web site,
enter this number in your profile to gain access to the SYBYL software
download section.

Exit SYBYL
• A System Info button presents more detailed information in the System

Messages area. This information is useful when you contact your Tripos
Support office.
2.6 Exit SYBYL

Exiting SYBYL means closing the SYBYL session. If you have multiple
sessions open simultaneously you must close each of them individually.
2.6.1 How to Exit SYBYL

Exit SYBYL in any of the following manners:
From the Menubar:

File > Exit
When exiting SYBYL via the menubar you will be prompted whether to save
the current session. If you choose not to save a session upon exit you will be
prompted whether to save molecules and spreadsheet that have not been saved
after the most recent modification.
In the Console:
Type: exit or quit.
When exiting SYBYL at the command line you will not be prompted whether to
save the session. You will be prompted whether to save molecules and spread-
sheet that have not been saved after the most recent modification.
2.6.2 End the Tutorial

¾ File > Exit
You are presented with the opportunity to save the session. A SYBYL session
ends when SYBYL is exited. The current state of a SYBYL session can be
saved and reloaded at a later time. See Manage SYBYL Sessions on page 183
for more details. If you choose not to save a session upon exit you will be
prompted whether to save molecules and spreadsheet that have not been saved
after the most recent modification.
For this tutorial, do not save the session.
¾ Click Don’t Save.
SYBYL closes.

Starting SYBYL and Setting its Environment
2.7 Starting SYBYL and Setting its Environment

There are several ways to access SYBYL. Each serves a different purpose. You
will find all access modes on the SYBYL-X 1.1 look-aside menu in your
computer’s list of programs or applications.
2.7.1 Standard SYBYL-X Startup

The easiest way to start SYBYL is via the desktop icon, , if it was placed
there during software installation.
The standard SYBYL application includes a menubar, toolbars, a graphics

window, a command console, and a system messages area. See The SYBYL
Window on page 25 for a full description.
If there is no SYBYL icon on your desktop, launch SYBYL as follows:
Windows:
• All Programs > SYBYL-X 1.1 > SYBYL-X
Linux:
• Applications menu > SYBYL-X 1.1 > SYBYL-X
• Or, in a system shell, type: trigo sybylx1.1
2.7.2 SYBYL-X Plus Console

You may start SYBYL with an additional, separate system console. Although
you may not type in this console, a small amount of information will be directed
to it by most SYBYL “db” commands (described in the UNITY Manual). Infor-
mation in this console may be useful for debugging purpose.
To launch SYBYL with the additional system console:
Windows:
• All Programs > SYBYL-X1.1 > SYBYL-X Plus Console
Linux:
• Applications menu > SYBYL-X1.1 > SYBYL-X Plus Console

Starting SYBYL and Setting its Environment
• Or, in a system shell, type:

trigo -shell sybylx1.1
sybyl -xterm
2.7.3 SYBYL-X Command Line

You may start SYBYL for use of its command line operations only. In this
mode only the command console is available. The SYBYL graphics window,
menubar and toolbars are not displayed.
To launch SYBYL in command mode only, without the graphics window:
Windows:
• All Programs > SYBYL-X1.1 > SYBYL-X Text Console
Linux:
• Applications menu > SYBYL-X1.1 > SYBYL-X Text Console
• Or, in a system shell, type:
trigo -shell sybylx1.1
sybyl -text
2.7.4 SYBYL-X Environment Shell

A large number of applications that are accessible from within SYBYL may
also be run in standalone mode. Examples of these are the “db” commands
(UNITY Manual), Surflex-Dock and Surflex-Sim, among others. All that is
required to run these applications is a system shell in which SYBYL’s
environment variables have been defined.
To open a system shell in which the SYBYL environment has been defined:
Windows:
• All Programs > SYBYL-X1.1 > SYBYL-X Environment Shell
Linux:
• Applications menu > SYBYL-X1.1 > SYBYL-X Environment Shell
• Or, in a system shell, type: trigo -shell sybylx1.1

Chapter 3.
The SYBYL Window
When SYBYL starts its main window is presented. The graphics window
contains the menubar, toolbar icons, and the display area. The console is docked
below the display area.
All layout changes you make are preserved in .sybyl/windowState within

your home directory or folder.
• The SYBYL Menubar on page 26

• SYBYL Menus
• Menu, Dialog, and Mouse Shortcuts
• The SYBYL Toolbar Icons on page 29
• The SYBYL Textports on page 30
• Special Keyboard Keys on page 32

Chapter 3. The SYBYL Window
The SYBYL Menubar
3.1 The SYBYL Menubar

A SYBYL menu option can:
• be a simple command: Edit > Delete Everything
• lead to submenus: View > Hydrogen Bonds > Intermolecular
• open a dialog: File > Open Session...
When you initiate an operation by clicking a menu item, no other operation is

possible until either that operation has finished or until you cancel it. All
menubars are greyed out while the current operation is active.
3.1.1 SYBYL Menus

Each list of menu options can be detached from the menubar so that it remains
visible even after a selection is made.
• To detach a menu: click the dashed line above the first item.
• To close a tear-off: click the X in the upper right corner.
File Contains options to load information for display in

SYBYL. It also has options for operations such as sav-
ing files, creating Molecular Spreadsheets, editing text
files, managing sessions, and exiting SYBYL.
Edit Focus on creating and modifying structures in the
SYBYL display. It contains options for operations such
as clearing the screen, sketching, modifying, copying,
merging, and extracting structures.
View Options affecting the visualization of structures in the
SYBYL display. It contains options for operations such
as coloring, labeling, hiding, managing backgrounds,
surfaces, and monitors and accessing the 2D Viewer.
Tools for measuring are also found here.
Compute SYBYL’s minimization and dynamics tools can be
accessed. It contains options for calculating charges,
loading force field parameters and conformational
searches. This menu also contains options for analyzing
the results of the calculations, defining aggregates, and
defining constraints.
Applications Accessing the specialized tools and techniques offered
by Tripos for use in SYBYL. Tools for matching and
fitting are also found here.
Biopolymer Functionality specific to biopolymer structures

The SYBYL Menubar
UNITY Tools for performing various types of database

searches.
Options Access to the interface for setting tailor variables. The
default molecule area and directory can be changed
from this menu and various lists and information can be
obtained. Functionality for recording and playing back
command sequences is also available.
Help Options for accessing the Tripos Bookshelf (HTML
version of the SYBYL documentation). Release notes
and other information about the current version are also
available from this menu.
See the SYBYL Menubar to Command Mapping (accessible from the Tripos
Bookshelf’s main page) to find a complete listing of options for each menu
item, with links to descriptions and corresponding commands.
3.1.2 Menu, Dialog, and Mouse Shortcuts
Menu Shortcuts
You can navigate within the SYBYL menu use the keyboard.
1. Press the keyboard Alt key while typing the underlined letter corresponding
to the menu of interest. For example, Alt-E opens the Edit menu.
2. Once a menu is open:
• Simply type the underlined letter associated with the item of interest.
• Use the keyboard arrow keys to navigate within the menu.
• Press the keyboard Enter key to activate the highlighted menu item.
Dialog Shortcuts
Within a dialog:
• Press the keyboard Tab key to skip to the next field or item in a list.
• Use the keyboard arrow keys to move up or down in a list.
• Use the mouse’s scroll wheel to select an item in a pull-down menu or to
move a slider’s position.
• In a dialog containing a single list of option, double-click an item to
select the option and close the dialog.

The SYBYL Menubar
Where is the dialog?

If SYBYL seems unresponsive, it may be because the active dialog has
become hidden by another window.
Click (stack windows) to bring the active window in front of the
display area.
Mouse Shortcuts
The following shortcuts involve the mouse:

• If your mouse has a scroll wheel you can use it in the graphics area to
zoom in and out. This scaling action applies to all objects, whether
visible or temporarily hidden.
• Right-click on the following objects to display relevant context menus:
• an atom
• a surface or ribbon
• the SYBYL backdrop
Use the mouse with keyboard keys to make selections and to move objects.
• Selecting With the Mouse on page 62

The SYBYL Toolbar Icons
3.2 The SYBYL Toolbar Icons

Use the icons in the SYBYL toolbars to interact with the graphics.
A toolbar can be docked under the menubar or to either side of the display area
or it can be “torn off” so that it exists as its own window. Simply click the line
in front of a group of icons and dragging the toolbar to its new location.
To activate an icon, click it. Any dialogs that are displayed can remain open as
you work or you can close them by clicking the X in the upper corner or their
window.
Standard
Edit
View
Display
Molecule
Selection
Transformation
Biopolymer
Mouse Mode
Miscellaneous

The SYBYL Textports
3.3 The SYBYL Textports

Two text areas are docked within the main SYBYL window, initially below the
graphics window. Use the sash to re-apportion the space given to each.
1. Command Console
This area contains the interactive SYBYL prompt (SYBYL>). Type any
SYBYL command at the prompt to execute it immediately. When the
operation completes the SYBYL prompt will reappear. See the List of
SYBYL Commands in the Reference Guide.
2. System Messages
This area contains the text output of system operations. A few SYBYL
functions report information in this area. You may also type simple system
commands in the Command Console (e.g. cmd ls to list the files in the
current directory or folder). The output of such a command appears in the
System Messages area.
To detach the command console or the system message area click its icon.
To re-dock a detached window, drag its title bar to any edge within the SYBYL
graphics window.
3.3.1 Typing Commands in the Console

Although most SYBYL functions are available via the menubar and toolbars,
you may need or prefer to type some SYBYL commands in the command
console.
You may enter a command and all its options on a single line. Only the shortest
unique string needs to be typed to identify a command or any of its arguments.
If you type only the command name then press Enter, you will be prompted for
the necessary arguments with default values in angle brackets.
SYBYL has two modes for command operations:

• In the standard mode, commands are entered in the console but object
selections can also be done via the “expression” dialogs. Pressing the
Enter key after each argument will display the appropriate dialog when
an object selection is required.
• You may also switch to a mode in which once a command name has
been typed its remaining arguments must be entered in the console
To activate full command mode type: SET PICKING NO_PICKING
To return to the standard mode, type: SET PICKING OBJECT_ONLY

The SYBYL Textports
3.3.2 Special Characters

When interacting with SYBYL in the Command Console use the following
characters:
• ?—Use the help character at any time to obtain information about a
command, the values of an argument, or the format of a specific
parameter.
• ^ (caret)—Use the abort character in response to any prompt to
terminate the command operation. No changes are made to the
molecule(s).
• | (vertical bar)—Use the end loop character to terminate the entry of
parameters being requested in an indefinitely repeating loop. When you
have completed all the required entries, respond to the next prompt with
the end loop character. SYBYL terminates the request loop and moves
on to the next parameter.

Special Keyboard Keys
3.4 Special Keyboard Keys

Key Action
F1 Help
F7 Toggle hardware stereo on and off. F7 is active only if
the necessary hardware is available. See Hardware Ste-
reo in the Installation and Administration Manual.
F9 Toggle mouse focus between Global and D1.
F10 Toggle between Global and D2.
Ctrl + Up arrow Rotate all displayed objects +90° about the X-axis.
Ctrl + Down arrow Rotate all displayed objects –90° about the X-axis.
Ctrl + Left arrow Rotate all displayed objects +90° about the Y-axis.
Ctrl + Right arrow Rotate all displayed objects –90° about the Y-axis.

Chapter 4.
Open and Save Files of Molecules
• Open Files via the Menubar on page 34

• Save a Molecule File via the Menubar on page 39
• Open/Save Mol2 Files via the Command Line on page 41
• Open and Save in Other Formats on page 42
• Convert Between Molecular File Formats on page 44
• View and Edit Text Files in SYBYL on page 49

Chapter 4. Open and Save Files of Molecules
Open Files via the Menubar
4.1 Open Files via the Menubar

The SYBYL file browser presents slight differences depending on context:
• Open a file to import it into SYBYL: File > Import File ( ). A
molecule area is often associated with that operation.
• Open a SYBYL session: File > Open Session ( ). Each saved
SYBYL session consists of many files stored in a directory with the .ses
extension.
• Save an image to a file: File > Save Image.
Common Features
Directory The currently selected directory. The pull-down pro-

vides access to the parent directories.

Toolbar
• —Go back to the previously selected directory.
• —Go up one level in the directory tree, that is,
the parent directory.
• —Delete the file(s) selected in the list.
• —Create a new directory/folder within the
currently selected directory. This button is disabled
if you do not have permission to write to the
selected directory (e.g. the demo directory).
Bookmarks Provides quick access to commonly used directories.
By default, the current working directory (identified by
the variable $CWD), your home directory (identified as
$HOME), and SYBYL’s demo directory (set by the
variable $TA_DEMO) are listed. If you changed direc-
tory while in SYBYL, the variable $PWD identifies the
directory in which you started SYBYL.
• To add another directory to the list, navigate to that
directory then press the button.
• To remove a directory from the list, click that
directory and press the button. (Note that the
default bookmarks cannot be removed.)
User-defined bookmarks are stored and can be directly
edited in the $HOME/.sybyl/directory_bookmarks
file.
Note: You can resize the list of bookmarks by moving
the horizontal sash.
Directory Navi- Select one of the sub-directories if you want to select a
gation file from it.
Note: a vertical sash to the right of this list allows you
to widen this section of the dialog.
Selection List all files of the specified format in the selected
directory. You may retrieve multiple files at once by
holding the Ctrl key while selecting the desired files.

On File > Import File
File to read The name(s) of file(s) selected to be read in. You may
type a subdirectory name or a full directory path and
press OK to list the files it contains. You may also type
the name of a file.
For MDL SD or MOL files, normalization (aromatiza-
tion and standardization) of the structures is done by
default. To control this default behavior, use the com-
mand TAILOR SET TABLE MDL_NORM_AROM.
The label for this field varies depending on how this
dialog was invoked. For example, if the dialog was dis-
played using File > Database > Open, this field is
labeled Databases.

Files of Type • Molecule—Lists files containing molecules (e.g.,

.mol2, .pdb, .sln, .hits, . sdf, .cry,…). Selected
file(s) will be loaded into molecule areas. Files of
type SLN and SD are loaded into spreadsheets. If a
Mol2 file contains multiple molecules, you will be
given the choice to load the contents into an MSS or
separate molecule areas.
• SYBYL Mol2—Lists files with the .mol2
extension. Selected file(s) will be loaded into
molecule areas. If a file contains multiple
molecules, the Multi-Mol2 File Detected dialog is
displayed asking whether to load the contents into
an MSS or molecule areas.
• SLN—Lists files with the .sln and .hits extensions.
Selected file(s) will be loaded into MSSs, one for
each file. A file of type SLN must start with the
line:
#SYBYL/3DB HITLIST
• MDL-SDF—Lists only MDL .sdf files; a data
format that can contain multiple chemical structures
and arbitrary data associated with those structures.
Selected file(s) will be loaded into MSSs, one for
each file.
• PDB—Lists files containing proteins (e.g., .pdb,
.ent, …). Selected file(s) will be loaded into
molecule areas.
• Sequence—Lists files containing sequences (e.g.,
.pir, .fast). Selected file(s) will be loaded into
molecule areas and into the Sequence Viewer.
• Spreadsheet—Lists files that can be loaded into a
spreadsheet (e.g., .tbl, .tsv, .csv, .hits, .sln, .3db,
.sdf, and .chom (created by Legion)). Selected
file(s) will be loaded into MSSs, one for each file.
• Database—Lists database files (e.g., .tdb,
.mdb). Selected file(s) will be loaded into MSSs,
one for each file.
• Any File—Lists all entries in the selected
directory. SMILES files can be selected and opened
using this option.
Other options may appear in this pull-down depending
on how this dialog was invoked and the type of object
being opened.

Molecular Areas List of molecule areas and names of any currently dis-
played structures. By default, SYBYL automatically
selects the first available molecule area. If multiple files
are selected, molecules are loaded in consecutive mole-
cule areas.
(Note that there are cases when this list is disabled, for
example, when opening a database (File > Database >
Open)).
On File > Open Session

See Manage SYBYL Sessions on page 183 for additional information.
Directory Name of the session directory selected at the top of the

dialog.
Files of Type Session (*.ses)
On File > Save Image

See Image - Save to FIle, Copy to Clipboard in the Graphics Manual for
additional information.
Filename Enter the name of the file to be created.

Files of Type • JPEG File (*.jpg *.jpeg)
• Bitmap File (*.bmp)
• PNG File (*.png)
• TIFF File (*.tif *.tiff)
Image Dimen- The Width and Height of the image as captured are
sions reported in Inches and Pixels for the specified DPI
value (default is 300). You may modify these before
saving the image to a file. Note that these values are
interdependent and that the proportions will be main-
tained. After modifying a value, press the Enter key to
effect the change.
JPEG Options The Quality Slider provides an image compression
mechanism.
• Load Molecules on page 16 for an example exercise.
• Image - Save to FIle, Copy to Clipboard in the Graphics Manual

Save a Molecule File via the Menubar
4.2 Save a Molecule File via the Menubar

Use the File > Export File ( ) option to save one or more molecules. By
default, SYBYL saves the selected molecule(s) in the specified format to the
current working directory. What is saved with the file depends on the file type.
Only the selected molecules are saved, not associated background images, if
any are present.
File Name for the file being saved. You can accept the default,
enter a new file name, or specify a different directory via
the [...] button.
Acceptable file names:
• 3 to 15 alphanumeric characters
• May include _ (underscore) or a - (hyphen)
A default extension for the specified file format will auto-
matically be added to the filename. Therefore, do not
include a (.) period in your filename, unless you are enter-
ing an extension.
Format Select the file format.
Note: You can save multiple structures in a single file when
you use Mol2 and MDL-SDF.
Molecule List Use the buttons (Select All, Invert, and Clear) to select
the molecules to save. The dialog reports the total number
of selected molecules and the total number of molecules in
the list.
Mol2 Files
SYBYL uses Mol2 files to store molecules resulting from most computations.

Save a Molecule File via the Menubar
Mol2 files are text files containing all information necessary to reconstruct the
molecule. The format is based upon the convention of a keyword for each type
of data needed to reconstruct the molecule, followed by a group of records. (See
the Mol2 File Format chapter in the Toolkit Utilities Manual.)
Colors are also saved. Additionally, any defined sets or features are saved to the
Mol2 file.
Default Names for Unnamed Molecules

All molecules stored in a Mol2 file must have a name. This name is usually
provided by the context of the operation or by the use via Edit > Molecule >
Name.
The command TAILOR SET MOL AUTO_NAME determines how to handle

unnamed molecules:
• YES: unnamed molecules (single and MultiMol2) are named according
to the filename.
• NO: unnamed molecules are named “unnamed”.
• Save a Molecule to a File on page 20 for an example exercise.
• Read and Write PIR and FASTA Files in the Biopolymer manual.
• Read and Write PDB Files in the Biopolymer manual.
• TAILOR SET PDB in the Tailor manual.
• SLN Files on page 42
• SD/MDL Mol Files on page 42

Open/Save Mol2 Files via the Command Line
4.3 Open/Save Mol2 Files via the Command Line

MOL direction [mol_area] [filename]
direction • DIRECTORY—Report if specified file has Mol2 format, list

molecule(s) in the file, plus the number of atoms and bonds.
• IN—Read file containing a single molecule.
• MULT_IN—Read file containing several molecules, starting at
the specified area and filling subsequent areas thereafter,
until all molecules are read. Use DATABASE ADD to insert
molecules into a new database.
• MULT_OUT—Write file containing several molecules in
several molecule areas.
• OUT—Write file containing a single molecule in specified
area.
mol_area Molecule area to receive input data (IN, MULT_IN) or that con-
tains molecule(s) to write to a file (OUT, MULT_OUT) or to the X
clipboard (XCOPY, XPASTE). Contents of molecule areas are
overwritten.
filename File to read/write. When writing a file, if the filename already
exists, it is overwritten.
• Open Files via the Menubar on page 34

Open and Save in Other Formats
4.4 Open and Save in Other Formats

4.4.1 SLN Files
Menubar:
File > Import File ( ) (specify the File Type as SLN)
File > Export File ( ) (specify the Format as SLN)
When a file that contains SLNs is opened, its contents are loaded into an MSS.
4.4.2 SD/MDL Mol Files

The formats of an SD file and an MDL Mol file are published by Molecular
Design Ltd. (MDL). SD files have a default extension of .sdf. MDL Mol files
have a default extension of .mol.
Read/Write SD/MDL Mol Files
Menubar:
File > Import File ( ) (specify the File Type as MDL-
SDF)
The contents of an MDL MOL file are loaded into a mole-
cule area. The contents of an MDL SD file are loaded into
an MSS.
File > Export File ( ) (specify the Format as MDL-
SDF)

Open and Save in Other Formats
Command Line: MDLMOL IN|OUT|MULT_IN|MULT_OUT mol_area

filename(s)
• IN—Read an MDL Mol file. Assign correct atom and
bond types (verify that they are correct before
proceeding). Non-recognized atoms are assigned
SYBYL’s type DU (dummy). Files with more than 999
atoms or bonds cannot be read. Note that normalization
(aromatization and standardization) of the structures is
done by default. To control this default behavior, use
the command TAILOR SET TABLE MDL_NORM_AROM.
• OUT—Write a MDL Mol file. Use the molecule’s name
as the file header name, and prompt for the header and
comment line. SYBYL aromatic bonds are converted to
alternating single and double bonds. SYBYL dummy
atoms (DU) and lone pairs (LP) are removed from the
atom list before file is written.
• MULT_IN—Read an SD file.
• MULT_OUT—Save multiple molecules to an SD file.
Note: To include hydrogens when saving to an SD or MDL Mol file, use

TAILOR SET TABLE MDL_H_HANDLING to KEEP_ALL.
Convert MDL Mol Files to Molecular Spreadsheet or UNITY Hitlist
Menubar:
File > Import File ( ) (specify the File Type as MDL-
SDF). The contents of an MDL MOL file are loaded into a
molecule area. The contents of an MDL SD file are loaded
into a spreadsheet (MSS).
File > Export File ( ) (specify the Format as SYBYL
Table or UNITY Hitlist)
Command Line: MDLMOL_CONVERT HITLIST|MSS input_file
name_field output_file
• input_file—Name of MDL Mol file to translate.
• name_field—Registration/Name field to look for in
MDL Mol file (case sensitive).
• output_file—Name to assign to hitlist file or table
generated.

Convert Between Molecular File Formats
4.5 Convert Between Molecular File Formats

Convert molecular descriptions from one file format to another, performing
some additional operations during the conversion process.
For the expert: utilities described in the UNITY Manual

• dbtranslate: Translate between Molecule Formats
• sln2img: Translate SLN or SMILES Files to PNG or GIF
UNITY > UNITY Tools > Translate Molecular Files

or
File > Translate Molecular Files
Input Options
Enter SLN SLN for input structure.

Mol Area Molecule area containing structure.
File Type of input file: SLN, BCD (BinConf) (binary con-
formational data file), MDL-SDF, Original SMILES,
Daylight SMILES, Conversational SMILES, SYBYL
MOL2. Enter full path for file. (Press [...] to browse.)
(Read about Binary Conformational Data Files in the
UNITY Manual.)

Output Options
SLN to Textport Print SLN in the console.

Mol Area Display structure on screen. Select molecule area from
the pull-down.
File Save results to file of specified type: SLN, BCD (Bin-
Conf) (binary conformational data file), MDL-SDF,
Original SMILES, Daylight SMILES, Conversa-
tional SMILES, SYBYL MOL2, SLN Tabs (gives
regID, a tab, then SLN, if the input is BCD, then the
regIDs and number of conformations are provided in the
output file). Enter full path for file.
For BCD (BinConf), if the specified file exists, infor-
mation will be appended to it (i.e., the contents will not
be overwritten). Read about Binary Conformational Data
Files in the UNITY Manual.
Specify Options Display the Translate Molecular File Options dialog for
further translation choices.

4.5.1 Specify Translation Options

UNITY > UNITY Tools > Translate Molecular Files
In the Translate Molecular File dialog, press Specify Options.
Generate Concord 3D Use Concord to generate 3D coordinates. (Read

Coordinates about the use of Concord for this operation in the
UNITY Manual.) Enter the number of structures
to give to Concord per batch in the Batch Size
field. Default is 500.
Perceive Chirality at Check for the chirality of carbon atoms based on
Carbons 3D coordinates or, if coordinates are not present,
bond stereo flags. Existing chirality attributes
that perception determines are incorrect, will be
removed. (Not recommended for 2D SD files.)

Perceive Chirality at N Set chirality for nitrogen and phosphorus atoms

and P based on 3D coordinates or, if coordinates are
not present, bond stereo flags. Existing chirality
attributes that perception determines are incor-
rect, will be removed. (Not recommended for 2D
SD files.)
Perceive Bond Stere- Set double bond stereo based on 3D coordinates
ochemistry or, if coordinates are not present, bond stereo
flags. Use the environment variable
PERCEIVE_RING_BONDS to control how stereo
bond attributes are perceived in rings. Existing
stereo attributes that perception determines are
incorrect, will be removed. (Not recommended
for 2D SD files.)
Include/Strip Property Turn on to include property data.
Data
Standardize Structures Check to enable standardization of structures by
using rules defined in standard.defs (by
default). (Read about Standardizing Structures in
the UNITY Manual.)
Standardization Rules Specify a different file to use for standardization
File rules.
Output for SYBYL Force output to be “SYBYL friendly.” Only six
Compatibility membered rings are aromatized, and charge sep-
arated nitro groups are converted to N(=O)=O.
Two files residing in the UNITY tables direc-
tory (path set by TA_FILE_PATH) are used,
mol2_arom.defs (special version aromatic-
ity.defs), and mol2_standard.defs (special
version of standard.defs).
Fill Valences Fill valences of translated structure.
Aromatize Structures Automatically perform aromatic normalization.
Convert to Kekule Include aromatic bonds in MDL file. Only avail-
able when output file type is MDL-SDF.
Validate Valences • Off—Prevent validation of structures.
• Warning—Validate structures, but do not
write invalid structures to a file.
• Error—Validate structures and save invalid
structures to designated file.
Invalid Structures File File to hold invalid structures. Only valid if Vali-
date is set to Error.

Treatment of H’s in How to handle hydrogens. Only valid when out-

MDL-SD Files put type is SD File.
• chiral_only—Keep hydrogens located on
chiral atoms (default and MDL compatible).
• remove_all—Remove all hydrogens.
• keep_all—Keep all hydrogens.
• carbon_remove—Remove all hydrogens
located on carbons.
MDL-SDF Field to use Data label within a MDL SD file identifying reg-
for Regid istration name. Only valid when input file type is
SD File.
Expand Macro Atoms Replace macro atoms with constituent atoms,
essentially exploding them.
Unique Structures Canonicalize translated structure.
Split SLNs over Multi- Turn off to generate a single line SLN. Only
ple Lines valid when output file type is SLN.
Fast Translation Use with Split SLNs over Multiple Lines to
convert hitlist to/from multi-line SLN output.
Only valid with SLN hitlists. Hitlist header infor-
mation is preserved or created (if not present).
Include/Strip Atom Turn on to include chirality.
Chirality
Include/Strip Stereo When off, stereo bond attributes are stripped.
Bonds Attrs Removal of stereo bond attributes occurs prior to
stereo bond perception, when Perceive Bond
Stereochemistry is on.
Include/Strip 2D Coor- Turn on to include 2D coordinates.
dinates
Include/Strip 3D Coor- Turn on to include 3D coordinates.
dinates
Visual Report of Display progress information on host terminal.
Progress
Report_Interval Number of structures to translate before report-
ing progress information. This option has no
effect unless Visual Report of Progress is on.
Enable/Disable Debug Turn on to display debugging messages.
Mode
Write Errors to Log Name of log file to hold errors. Default is
File dbtranslate.log. Existing file is overwritten.

View and Edit Text Files in SYBYL
4.6 View and Edit Text Files in SYBYL

To edit text files using a text editor, select Edit > Text File from the SYBYL
menubar. In the Edit File dialog, select the desired file. (The text editor can also
be displayed using the SPL expression generator, %file_edit.)
After you have specified the file to edit:

1. If you have the environment variable $EDITOR defined, it will preferen-
tially use that editor to edit. (Note: If $EDITOR is defined as vi or vim, it
will spawn an separate system shell.)
2. If $EDITOR is completely undefined, it will use the SPL editor.
$EDITOR does not have to be defined at the system level, you could define it in
SYBYL using setvar or in the sybyl.ini file (in your home directory):
setvar EDITOR nedit
The SPL editor is described below.
Save Save any changes made in the text field to the original
file.
Cancel Ignore any changes made in the text field and closes the
text editor.

View and Edit Text Files in SYBYL
Save As Specify a new location and/or file name in the Save

Text File dialog.
Search Search for the specified string entered in the displayed
dialog.
Again Locate the next occurrence of the search string.
Cut Remove highlighted text and place on the clipboard.
Copy Copy highlighted text to the clipboard.
Paste Paste text on the clipboard at the location of the cursor.

Chapter 5.
Understand Molecule and Display Areas
• What are Molecule and Display Areas? on page 52

• Change the Default Molecule Area on page 54
• Copy Between Molecule Areas on page 55
• Merge Molecule Areas on page 56

Chapter 5. Understand Molecule and Display Areas
What are Molecule and Display Areas?
5.1 What are Molecule and Display Areas?

A display area is where your molecule is displayed on the screen. SYBYL has
four unique display areas: D1, D2, D3, and D4.
Click the icon and select from the pull-down or click the icon to open
the Display Options dialog and use the Screen options to change the placement
on the screen. The figure below shows how molecules are displayed for each
Screen option.
Figure 1 Screen Modes for Display Options
A molecule area is a region of memory that holds a particular molecule. The

total number of molecule areas does not have a fixed limit, because the number
depends on your computer’s memory.
Note that molecule areas have rules:

• M1 is always in display area D1.
If you use additional molecule areas, they recycle through the display areas:

What are Molecule and Display Areas?
The figure below demonstrates this pattern.
Figure 2 Display and Molecule Areas
• Load Molecules on page 16 for an example exercise.
• Change the Display on page 16 for an example exercise.

Change the Default Molecule Area
5.2 Change the Default Molecule Area

The default molecule area is M1.
Tip: If you are performing a number of operations on a structure in a different

area (for example, M3), you can change the default to that area (M3), while
working on that structure.
Menubar: Options > Set > Default Molecule Area

Command Line: DEFAULT mol_area
The default molecule area is reported in the status bar at the bottom of the
SYBYL window.

Copy Between Molecule Areas
5.3 Copy Between Molecule Areas

When items are copied between molecule areas, the source molecule area
remains unchanged and the target area contains the copy.
Copy the Contents of one Molecule Area to Another
Menubar: Edit > Copy

Acts only on pre-selected atoms in a single molecule
area.
Icon:
on the Edit toolbar.
Command Line: COPY origin_atomexp target_area
• origin_atomexp—Molecule area to duplicate (e.g.,
M1) or atom expression (e.g., M1(1,2,3,5,10) for
atoms to duplicate.
• target_area—Molecule area to receive the duplicate
structure/atoms.
Makes an exact copy of all selected contents (properties, colors, and associated
background images) in one work area and places the copy in another area. The
origin (source) molecule is not altered. The previous contents of the target area
(if any) are moved to the recovery stack for that area.
Extract Atoms and Associated Data Structures to a Different Molecule Area
Menubar: Edit > Extract

area.
Command Line: EXTRACT atom_expr target_mol_area
Extracted atoms are removed from the origin area and replace the contents of
the target area (by default the first empty molecule area). All local set defini-
tions associated with the extracted atoms are copied to the new area.
If atom_expr does not specify a work area, the default work area is used.
If atomic charges are present in the target molecule before the extraction, the
atoms still bear the same charges after the extraction. However, they are marked
invalid, and will not be used on subsequent SYBYL operations. Validate these
charges manually via the command: CHARGE mol_area VALIDATE YES.

Merge Molecule Areas
5.4 Merge Molecule Areas

Merging combines a copy of selected atoms in the source molecule area with
the contents of the target area.
Unique Atom: The following scenarios define a unique atom:

• If the coordinates and the atom types in both the source and the target
area are different, an atom is considered to be unique.
• If the coordinates in the source and the target area are the same, but the
atom types are different, an atom is considered to be unique.
• If the atom types in the source and the target are the same, but the
coordinates are different, an atom is considered to be unique.
You can set the distance within which two atoms are considered identical and
whether to keep only unique atoms with TAILOR SET MERGE.
Non-unique Atom: An atom in the source area with the same atom type and
coordinates as an atom in the target area. See Merging Non-Unique Atoms on
page 58
• Combine (Join) Two Molecules on page 135
• TAILOR SET MERGE to alter the characteristics of merging.
5.4.1 Merge Atoms and Associated Data Structures

Tip: If molecules have been rotated and/or translated, use View > Transfor-
mations > Freeze to transform the coordinates before merging.
Menubar: Edit > Merge

area.
Command Line: MERGE atom_expr target_area
If atom_expr does not specify a work area, the default
work area is used.
Check the output displayed in the console for messages about the merge.
Special conditions apply when merging non-unique atoms and features.
When you merge atoms and associated data structures, most of the associated
data structures are kept in the merge. These include:
• ATOM
• Atom type

• Atom alternate type (Amber/Kollman/MMFF94 types)

• Atom name
• Charges
• Atom ID is not kept.
• BOND
• Bond type
• Bond ID is not kept.
• SUBSTRUCTURE
• Substructure type
• Substructure name
• Substructure ID is not kept.
• CENTER_OF_MASS—If a CENTER_OF_MASS in the source area has
the same name as one in the target area, the one in the source area is not
merged.
• CENTROID—If a CENTROID in the source area has the same name as
one in the target area, the one in the source area is not merged.
• Constraints—If an atom associated with a constraint is not merged, the
constraint is also not merged. (Refer to the Constraint chapter in the
Force Field Manual.)
• FFCON_ANGLE
• FFCON_DIST
• FFCON_MULTI
• FFCON_RANGE
• FFCON_TORSION
• PLANE—If a PLANE in the source area has the same name as one in
the target area, the one in the source area is not merged. Since a plane
always has an associated NORMAL, if that NORMAL is not merged,
the PLANE is not merged.
• NORMAL—If a NORMAL in the source area has the same name as one
in the target area, the one in the source area is not merged.
• SET—Any set in the source area with the same name as the set in the
target area will be combined into a single set when merged.
Note: If CENTER_OF_MASS, CENTROID, PLANE, or NORMAL is defined

on a molecule, SYBYL creates dummy atoms representing features (e.g. center
of a centroid). These dummy atoms need to be selected for merging or the
whole feature information is not merged.

The associated data structures that are not merged include:

• ANCHOR_ATOM
• EXTENSION_POINT
• FF_PBC
• RING_CLOSURE
• ROTATABLE_BOND
• U_FEAT
• UNITY_ATOM_ATTR
• UNITY_BOND_ATTR
5.4.2 Merging Non-Unique Atoms

Normally there is nothing to merge if two atoms are “non-unique”. There are
some cases however, where they may be merged.
Non-unique atoms from the source area may be merged into the target area
when both of the following conditions have been met:
• The non-unique atom in the source molecule area has a unique atom
attached to it.
AND
• In the target molecule area there is no open valence on the atom corre-
sponding to the non-unique atom in the source molecule area.
The unique atom carries with it the non-unique atom to preserve the bonding
information.
Example: Merging Non-Unique Atoms
Read in a methane molecule into M1 and into M2. Then change one of the
hydrogens in the M1 methane molecule to bromine.
¾ Select METHANE and press OK.
¾ Select METHANE and press OK.
¾ Use on the Display toolbar to set the screen mode to Half.
¾ Edit > Atom > Modify

¾ In the Option dialog, select TYPE and press OK.
¾ In the Atom Expression dialog, click one of the hydrogen check boxes
and press OK.
¾ In the Option dialog, select Br and press OK.
Relative to M2, the carbon and hydrogens in M1 are non-unique atoms, while
the bromine is a unique atom.
Merging M1 into M2 will bring the non-unique carbon and the unique bromine
from the source area to the target area (M2).
¾ Double-click any atom in M1 to select the whole molecule.
¾ Edit > Merge
¾ In the Molecule Area dialog, select M2:methane and press OK.
M2 now contains 7 atoms. To verify the contents of M2:
¾ Options > List > Atoms
¾ In the Atom Expression dialog, select M2 from the pull-down at the top
of the dialog.
¾ Press .
¾ Press OK.
¾ In the Option dialog, select BRIEF and press OK.
The console reports something similar to the following:

Molecule area M2 Atoms
Molecule Name: methane
Number of defined atoms: 7
id name substructure type x y z charge

-- ---- ------------ ---- - - - ------
1 C1 METHANE C.3 0.0000 0.0000 0.0000 0.000
2 H1 METHANE H -0.2694 -0.7900 0.7164 0.000
3 H2 METHANE H 0.9250 0.4950 0.3308 0.000
4 H3 METHANE H 0.1572 -0.4444 -0.9939 0.000
5 H4 METHANE H -0.8128 0.7394 -0.0533 0.000
6 BR1 METHANE Br -0.4747 -1.3919 1.2622 0.000
7 METHAN+ METHANE C.3 0.0000 0.0000 0.0000 0.000
Number of atoms selected for listing: 7
¾ When finished, use the icon to reset the screen mode to Full.
¾ Edit > Delete Everything

Chapter 6.
Select Atoms, Bonds, or Substructures
• Selecting With the Mouse on page 62

• The Selection Menu and Icons on page 63
• General Description of the Expression Dialogs on page 67
• Tutorials:
• How to Use the Atom Expression Dialog on page 75
• How to Use the Bond Expression dialog on page 82
• How to Use the Substructure Expression Dialog on page 85
Selection of atoms, bonds, or substructures (such as residues in a protein) can be

as simple as clicking on the desired objects in the SYBYL display area. More
complex selection may be based on a particular type or a defined set, and may
use Boolean operations.
Many menubar and toolbar operations in SYBYL will operate on the current
selection in the display area. For example, selecting several atoms in the display
area and then clicking on the Display toolbar immediately changes the
rendering of the selected atoms (and connecting bonds) to be capped sticks.
• Formats for Specifying Objects on page 202.
• Create Complex Expressions on page 211.

Chapter 6. Select Atoms, Bonds, or Substructures
Selecting With the Mouse
6.1 Selecting With the Mouse

One-click selection:
• Click on an atom to select it. If the atom is spacefilled you must click in
the center of the sphere to select the atom.
• Click on a surface or ribbon to select it.
Select a residue or substructure:

• Double-click on any atom in a residue to select the entire substructure.
Select an entire molecule

• Triple-click on any atom to select everything in the molecule area. In the
context of a biopolymer complex, this means the biopolymer itself as
well as any ligand, cofactor, metal and waters in the same molecule area.
Select all atoms in a rectangular area

• Ctrl+Alt while dragging the mouse to select all atoms in the area
outlined by a rectangle.
Toggle the selection state of an object

• Ctrl+click an atom or surface to add it to or remove it from the current
selection.
• Ctrl+double-click any atom to toggle the selection station of its
substructure.
• Ctrl+triple-click any atom to toggle the selection state of the entire
molecule area.
Clear all selection

• Click anywhere on the SYBYL backdrop.
• Click .

The Selection Menu and Icons
6.2 The Selection Menu and Icons

On the SYBYL menubar: Selection
Usage Note: Atoms that are invisible cannot be selected and, therefore, cannot
be acted upon unless the operation affects the entire molecule area.
6.2.1 Expand the Selection

This functionality is enabled only if at least one atom has been selected.
Access:
• Menubar: Selection > Expand
• Icon: on the Selection toolbar.
To Anything The selection expands to include all atoms contiguously

Connected connected to the pre-selected atom(s).
For example, in a protein/ligand complex with a ligand
atom selected, expansion selects all atoms in that ligand
and none of the protein atoms nor any atoms in addi-
tional structures such as water, metal or other ligands.
To Substructure The selection expands to include all atoms in the sub-
structure(s) that contain pre-selected atom(s).
For example, in a protein with atoms selected in two
residues, expansion selects all atoms in those residues.
To Chain The selection expands to include all atoms in the pro-
tein chain(s) that contain pre-selected atom(s).

To Biopolymer The selection expands to include all biopolymer atoms

in the molecule area(s) that contain pre-selected
atom(s). Biopolymer atoms are those that fall in the
Residues listing of the Atom Expression dialog.
Examples given a solvated protein/ligand complex:
• If one protein atom is selected, expansion selects
the entire protein, but not ligand, solvent, or any
other non-protein atoms.
• However, if the waters are selected, expansion adds
all protein residues to the selection. The same apply
to a pre-selected ligand or cofactor.
To Structure The selection expands to include all atoms in all the
molecule areas that contain pre-selected atoms.
Within a Radius The selection expands to include atoms in all molecule
areas that are within the specified radius of pre-selected
atoms.
• For small molecules the expansion selects atoms
within the specified radius.
• For biopolymers the expansion includes all
substructures that have any atom within the
specified radius.
6.2.2 Invert the Selection

This functionality is enabled only if at least one atom has been selected.
Access:
• Menubar: Selection > Invert
Within Selected The atom selection is inverted, but only within the mol-
Molecule Areas ecule area(s) that contain selected atom(s).
Over All Mole- The atom selection is inverted over all molecule areas.
cule Areas For example, with two molecule areas occupied and
only a single atom selected, inverting the selection over
all areas selects all atoms in both molecule areas and
deselects the atom that was originally selected.
Of Molecule Inversion of the selection depends on the original selec-
Areas tion:
• For molecule areas that contain selected atom(s), all
atoms will be deselected.
• For molecule areas that do not contain selected
atom(s), all atoms will be selected.

6.2.3 Clear the Selection

Clear the selection from all objects. This feature is available only if at least one
object has been selected.
Access:
• Mouse: click the left button in an unoccupied area of the SYBYL
backdrop.
• Menubar: Selection > Clear
• Keyboard Shortcut: Ctrl+D
6.2.4 Select All or Specified Atoms
All Atoms
Select all atoms in all molecule areas.
Access:
• Menubar: Selection > All Atoms
• Keyboard Shortcut: Ctrl+A
Some Atoms in a Single Molecule Area

Launch the Atom Expression dialog. If multiple molecule areas are occupied you
will be prompted to select the one of interest. Only the atoms selected in the
dialog will be selected when the dialog is closed via its OK button.
Access:
• Menubar: Selection > Select Atoms
All Atoms in Specified Molecule Area(s)

Select all atoms in the molecule areas selected via the Molecule Expression
dialog. If only one molecule area is occupied all atoms within it are selected
automatically.
Access:
• Menubar: Selection > Select Molecules

6.2.5 Select Atoms in Biopolymers

The following options of the Selection menu make use of sets and the
macromol dictionary to select atoms in all molecule areas that contain
molecules of type “biopolymer” (protein, DNA, RNA, carbohydrate).
Biopolymer Use the {BIOPOLYMER} built-in set to select all

amino acids and nucleic acids.
Backbone Use the {BACKBONE} built-in set to select all back-
bone atoms in all molecule areas.
Sidechain Use the {SIDECHAIN} built-in set to select all
sidechain atoms in all molecule areas.
Ligand Use the {BIOPOLYMER(LIGAND} set to identify all
ligand atoms.
Note that ligand atoms in a molecule area that does not
contain any residues may also be identified by show
and hide operations. This is because copying or extract-
ing a ligand from, for example, a protein/ligand com-
plex into a new molecule area assigns the type
“biopolymer” to the new molecule.
Water Use the {WATER} set to select all water atoms in all
molecule areas.
Metal Use the {METAL} built-in set to select all metal atoms
in all molecule areas.
be acted upon unless the operation affects the entire molecule area. For
example, if only the protein and water atoms within a 5 Å radius of a ligand are
currently visible, the Selection > Water operation will select only the visible
waters, not all of them. A subsequent deletion of the selected atoms will delete
only those few visible waters, leaving all others invisible, but still present.
6.2.6 Select Hydrogens

The following options of the Selection menu use hydrogens as the basis for
selecting atoms in all molecule areas.
Non-Hydrogens Select all non-hydrogens in all molecule areas.

Hydrogens Select all hydrogens in all molecule areas.
Polar Hydrogens Use the {POSSIBLE_HBOND} built-in set to select
hydrogens in all molecule areas.
Non-Polar Select all non-polar hydrogens in all molecule areas.
Hydrogens

General Description of the Expression Dialogs
6.3 General Description of the Expression Dialogs

Access:
• Menubar: Selection > Select Atoms
SYBYL’s Expression dialogs are designed to allow as much flexibility as

possible.
6.3.1 The Main Expression Dialog
As selections are made by clicking on The expression itself shows the mole-
objects in SYBYL’s display area or cule area and current “formula” that the
using the various buttons, an expression program will use to select the objects for
is formed. Activating the Show Atom the action being performed. As you
Expression check box will expand the become familiar with expressions, you
dialog so that the expression is visible. may enter them directly in the field. Note
that no atoms will be highlighted until
you press Apply.
The Expression dialog is presented under several different titles depending on

context: Atom Expression, Bond Expression, Substructure Expression, Sequence
Expression. Although the various Expression dialogs are very similar in layout,
there are differences. These differences are noted in the description below.

Molecule Area In the pull-down select the molecule area in which the
selection will be made.
Usage Notes:
• Picking from the screen is enabled only in this
designated molecule area.
• When the dialog is invoked via the icon
(Selection > Select Atoms), the molecule area is
set automatically to that of a pre-selected atom or, if
nothing had been selected, to the current default
molecule area as reported at the bottom of the
SYBYL window (set via Options > Set > Default
Molecule Area).
Hierarchy Contains a hierarchical representation of the structural
contents in the specified molecule area.
• When applicable, the different levels can be
expanded and collapsed by clicking the “+” and “-”,
respectively.
• Click an item in the hierarchy to select it (a check
mark appears in the check box). Atoms that are
hidden cannot be selected.
• When an item with subitems is selected, all its
subitems are also selected.
• When one or more subitems are selected, the check
box of the main item will contain a grey check mark
to indicate a partial selection.
• Right-click menus are available with options for
inverting the current selection. For proteins, the
menu options allow for various degrees of inversion
(e.g., invert the selection within the substructure,
within the chain, or the entire protein).
• If a protein has missing residues within a chain, you
will see multiple entries for that chain, one for each
continuous chain of residues. The residue number
range for each portion of the chain is shown in
parentheses.
Buttons to assist in selecting items in the hierarchy:
select all, invert selection, clear selection.
Selected Displays the number of objects that are selected in the
currently active molecule area.

Pick by In addition to selecting items in the hierarchy, the fol-

lowing options allow you to define selections based on
different categories of items (e.g., a particular residue
type, a predefined set, anything within a radius of an
atom, etc). Boolean operations are available for com-
bining the selections with any hierarchical selections.
• Atoms—Available only in the Bond Expression
dialog. Displays the Atom Expression dialog for
selecting bonds based on an atom expression.
• Substructures—Available in the Atom Expression
and Bond Expression dialogs when a protein is
displayed. Displays the Substructure Expression
dialog for selecting atoms based on residue, water,
or other defined substructure.
• Sets—Displays the Sets Selection dialog for basing
selection on defined sets, a radius, chirality, and/or
conformation. The options available depend on the
Expression dialog from which the Sets Selection
dialog is launched.
• Types—Displays the Types dialog for basing
selection on particular types of atoms, bonds, or
residues (depending on the Expression dialog from
which the Sets Selection dialog is launched).
Show Expres- Activate to expand the dialog to display a field contain-
sion ing the selection expression. Deactivate to collapse the
dialog by hiding the expression field.
You type a new or modify the existing expression in
this field. If you do, press Apply. See SYBYL Objects
and Their Expressions on page 197.
Create Set Defines a new set containing the selected items. Spec-
ify a name for the set. This new set is added to the list
of predefined sets in the Sets dialog. (Note: The new set
is temporary unless you save the molecule. Otherwise,
it is lost once the molecule is deleted from the display.)

Boolean Action The Boolean operators can be used to combine two

Buttons groups of selected items. These buttons appear only
when the Atom Expression or Substructure Expression
dialogs are accessed by clicking Pick by Atoms or
Substructures in another Expression dialog where
selections have been made.
• Intersect—Find the common items between the
selection identified in this dialog and the previous
selection. The remaining highlighted items are those
found in both groups of selected items.
• Remove—Subtract the items selected in this dialog
from the previous selection. The remaining
highlighted items are those found in the first group
of selected items, but not the second.
• Add—Add to the previous selection. The remaining
highlighted items are in either of the two groups of
selected items.
be acted upon unless the operation affects the entire molecule area. For
example, if only the protein and water atoms within a 5 Å radius of a ligand are
currently visible, the Selection > Water operation will select only the visible
waters, not all of them.A subsequent deletion of the selected atoms will delete
only those few visible waters, leaving all others invisible, but still present.
• Formats for Specifying Objects on page 202.
• How to Specify an Atom Expression on page 203
• How to Specify a Bond Expression on page 205
• Monomer Sequence Specification on page 208

6.3.2 Atom, Bond, Residue Types

The contents of the Types dialog depends on the Expression dialog from which
it was launched.
In an Expression dialog, press Types.
Atom Types Residue Types
Type List Lists available types for the atoms, bonds, or residues.
• The Atom Types dialog displays a hierarchy of atom
names and types. It functions the same way as the
Expression dialog hierarchy in terms of making
selections and expanding/collapsing lists.
• When bonds are being selected based on atom
types, all bonds connected to specified atoms are
highlighted.
• Bond types include: 1 (single), 2 (double), 3
(triple), am (amide), ar (aromatic), du (dummy),
un (unknown, cannot determine from the parameter
tables), nc (non-chemical).
• The Bond Types and Residue Types dialogs are
simple lists of types. Click multiple items to select
them. Click again to remove from the selection.
Sort Alphabeti- Sorts the list of residues alphabetically when turned
cally activated. Available only in the Residue Types dialog.


Buttons groups of selected items.
found in both groups of selected items. Available
only when a selection has been made in the
Expression dialog from which this dialog was
launched.
of selected items, but not the second. Available only
when a selection has been made in the Expression
dialog from which this dialog was launched.
• Add—Add to the previous selection. The
selected items.
• General Description of the Expression Dialogs
6.3.3 Sets for Atom, Bond, and Substructure Selection

The contents of the Sets Selection dialog depends on the Expression dialog from
which it was launched. Although the various Sets Selection dialogs are very
similar to each other in layout, there are differences. In the dialog description
below, these differences are noted.
In an Expression dialog, press Sets.
Atom Sets Substructure Sets

Chirality Selects a set of atoms that have a particular chirality.

Available only in the Sets for Atom Selection dialog.
Sphere Selects a set of atoms that fall within the specified
radius of currently selected atoms. Available in the Sets
for Atom Selection and Sets for Substructure Selection
dialogs.
Built-In Sets Selects atoms that belong to a particular built-in set.
(Note that the Rings option will identify internal and
external ring systems.) See Built-in Sets on page 223
for definitions of these sets. Available in the Sets for
Atom Selection and Sets for Bond Selection dialogs.
Sets Selects atoms that are part of a global or local set. Use
the Ctrl key to select multiple items in the list. See
Local Sets on page 220 and Global Sets on page 217 for
more information.
Conformations Selects substructures that form a particular conforma-
tional state in a protein. This list contains residue con-
formational states as defined in the macromol
dictionary. See the Dictionary Files description in the
Biopolymer Manual. Available only in the Sets for Sub-
structure Selection dialog.
Buttons groups of selected items.
• Add—Add to the previous selection. The remaining
selected items.
found in both groups of selected items. Available
only when a selection has been made in the
Expression dialog from which this dialog was
launched.
of selected items, but not the second. Available only
when a selection has been made in the Expression
dialog from which this dialog was launched.
• General Description of the Expression Dialogs

6.3.4 Molecule Expression

The Molecule Expression dialog is used when the context calls for identifying a
molecule(s) on which to operate.
Molecule List List of currently displayed molecules.

Buttons to assist in selecting items in the list: select all,
invert selection, clear selection.
• General Description of the Expression Dialogs on page 67.

How to Use the Atom Expression Dialog
6.4 How to Use the Atom Expression Dialog

The purpose of this tutorial is to explore the functionality offered by the Atom
Expression dialog.
The topics specifically covered include:

• General Tools for Atom Selection on page 75
• Simple Atom Selection on page 76
• The Atom Expression on page 76
• Select Atoms by Type on page 78
• Select Atoms via Defined Sets on page 78
• Atom Selection Tools for Proteins on page 80
A Matter of Time: This tutorial requires 5 minutes of personal time.
6.4.1 General Tools for Atom Selection
Setup
It is always a good idea to clear the screen and reset the display before starting.
¾ > Delete Everything
¾ Click on the View toolbar to reset all rotations and translations.
Load dicloxacillin.
¾ In the Open File dialog set the Files of Type to SYBYL Mol2.
¾ In the list of Bookmarks select [$TA_DEMO].
¾ In the Directory Navigation list select example.mdb.
¾ In the Selection list select dicloxacillin.mol2 then click OK.

Simple Atom Selection
Invoke the Atom Expression dialog.
¾ Selection > Select Atoms or press .
¾ Ctrl+click a few atoms in the molecule.

The selected atoms are highlighted on the screen. In the dialog the check
boxes for the selected atom are flagged, and a line below the list reports the
number of currently selected atoms.
¾ In the Atom Expression dialog, press (Select All).

All 49 atoms are selected in the dialog and highlighted on the screen.
¾ Press (Clear Selection).

0 atoms are selected.
¾ Select any three atoms in the dialog or Ctrl-click to select them in the
molecule.
¾ Ctrl-click one of the three atoms a second time.
That atom is no longer selected or highlighted.
¾ Press the icon to invert the selection.

47 atoms are selected.
¾ Press to clear the selection.
Usage Notes:
• If multiple molecule areas are occupied, picking from the screen is
enabled only in the molecule area designated at the top of the dialog.
• When the dialog is invoked via the icon (Selection > Select
Atoms), the molecule area is set automatically to that of a pre-selected
atom or, if nothing had been selected, to the current default molecule
area as reported at the bottom of the SYBYL window (set via Options >
Set > Default Molecule Area).
The Atom Expression
Selected atoms are stored in an atom expression. This information is accessible

at the bottom of the dialog.
¾ At the bottom of the Atom Expression dialog activate the Show Atom
Expression check box.

¾ Click one atom in the molecule to select it.

The Atom Expression field echoes the atom’s ID number.
¾ Ctrl-click to select a few more atoms.

Each atom’s corresponding ID number is echoed within the parentheses in
the expression.

The expression acknowledges that nothing is selected: M1(empty).
¾ Press to select all atoms.

An asterisk (*) appears between the parentheses. This represents all atoms
in the molecule.
You can also type atom ID numbers directly into the field.
¾ In the expression field delete * then type 4,5,6,7 within the paren-
theses.
¾ Press Apply.
Nothing happens to the molecule until you press Apply. Four atoms are
highlighted.

¾ Press the icon.
¾ Deactivate the Show Atom Expression check box.
Refer to SYBYL Objects and Their Expressions on page 197 for a complete
description.
Select Atoms by Type

¾ At the bottom of the Atom Expression dialog, click Types to display a
list of atom types.
¾ Activate the O check box.
¾ Click the + to expand the O category.

All oxygen atom types defined within SYBYL are selected in the list.
¾ Press Add to return to the Atom Expression dialog.

The five oxygens are highlighted in the molecule and in the dialog.
So far, you have added atoms to your selection. Now try subtracting the
carbonyl oxygens to keep only the other two.
¾ Press Types.
¾ In the Atom Types dialog, click the + to expand the O category again.
¾ Activate the check box for O.2 in the list.
¾ Press Remove.
Only two oxygens remain selected.
Select Atoms via Defined Sets
SYBYL includes a wide variety of rule-based sets that can be applied to select
atoms. Examples of these are Aromatic, H-bonds, Backbone, Sidechain, Rings,
etc. See Built-in Sets on page 223.
1. Select all atoms that are aromatic.

¾ In the Atom Expression dialog, click Sets to open the Sets for Atom
Selection dialog.
¾ Activate the Aromatic check box and press Add.

All carbons in the phenyl ring are selected.
¾ Activate the Show Atom Expression check box.

The field below the list shows the expression that is used to locate all (*)
aromatic atoms: {AROMATIC(*)}. Set names must always be surrounded
by braces.
2. Locate all rings within this molecule.
¾ Press Sets.
¾ In the Sets for Atom Selection dialog, activate the Rings check box and
press Add.
Four rings are identified and the Atom Expression field has a defined
argument to locate all atoms within a ring.
3. Find all nitrogen atoms in rings.
You have already selected Rings in the Atom Types dialog, now select another
criteria.
¾ Press Types.
¾ In the Atom Types dialog, activate the N check box.
¾ Press Intersect.
The Intersect operator can be thought of as a true “AND” filter in that both
conditions must be met.
Two nitrogen atoms are now selected. This is because only two of the three
nitrogens are also part of a ring.
¾ In the Atom Expression dialog, deactivate the Show Atom Expression
check box.
4. This concludes the exercise.
¾ Press Cancel to close the Atom Expression dialog.

6.4.2 Atom Selection Tools for Proteins

Most of the time selections in protein involve residues. See the How to Use the
Substructure Expression Dialog on page 85 for examples.
There are times, however, when the selection must consist of atoms, not full
residues. The following exercise is one such example.
1. Clear the screen.
2. Load crambin from a file in SYBYL’s demo directory.
¾ In the Open File dialog set the Files of Type to PDB.
¾ In the Selection list select 1crn.pdb then click OK.
Select Atoms via Defined Sets
3. Invoke the Atom Expression dialog.
¾ Selection > Select Atoms or press .
4. Invoke an operation that requires an atom selection.
¾ In the Atom Expression dialog click on the PHE13 check box.
The 11 atoms in PHE13 are highlighted.
5. Find all atoms that are within a 4 Å sphere of any PHE13 atom.
¾ Press Sets.
¾ In the Sets for Atom Selection dialog activate Sphere and type 4 in the
field.
¾ Press Add.
All atoms within the specified radius are highlighted in the molecule. Notice
that the selection does not include complete residues.

6. In the dialog notice that some of the check boxes are colored to indicate partial
selection within the corresponding residues.
¾ In the dialog expand the hierarchy for any of the partially selected
residues to see the atom(s) selected within.
7. Reduce the current atom selection to sidechain atoms only. You will use a built-
in set defined for that purpose.
¾ Press Sets.
¾ In the Sets for Atom Selection dialog activate the Sidechain built-in set.
¾ Press Intersect.
19 atoms are selected: all sidechain atoms within a 4 Å sphere around any
PHE13 atom.
¾ If you are curious about the expression used to identify these atoms,
activate the Show Atom Expression check box.
8. Color the selected atoms. You can do this via the toolbar while the dialog is
open.
¾ Use the icon’s arrow to select and apply your favorite

contrasting color.
9. The SYBYL menubar is disabled while the Atom Expression dialog is open.
¾ Press OK to exit the Atom Expression dialog with the current selection.
This concludes the exercise.

How to Use the Bond Expression dialog
6.5 How to Use the Bond Expression dialog

A Matter of Time: This tutorial requires a couple of minutes of personal time.
6.5.1 Setup
1. Load dicloxacillin from a file in SYBYL’s demo directory.
¾ In the Open File dialog set the Files of Type to SYBYL Mol2.
¾ In the list of Directory Navigation select example.mdb.
¾ In the Selection list select dicloxacillin.mol2 then click OK.
2. Invoke a SYBYL feature that affects bonds.
¾ Edit > Bond > Modify Type
¾ Select TYPE and press OK.
SYBYL opens the Bond Expression dialog.

¾ If multiple molecules are currently on the screen, you must designate
the molecule area of interest at the top of the dialog.
6.5.2 Select a Bond on the Screen

¾ Hold the Ctrl key and click two atoms that are bonded to each other.
The corresponding bond is highlighted in the dialog. An information line below

the hierarchy reports that 1 bond is currently selected.
¾ To clear the selection click anywhere on the SYBYL backdrop or

press the icon in the dialog.

6.5.3 Select all Bonds Connected to an Atom

¾ In the Bond Expression dialog, press Atoms.
The Atom Expression dialog is posted and automatically set to the same
molecule area.
¾ Click on the nitrogen in the fused (β-lactam) ring system then press
Add.
The three bonds between the nitrogen and its highlighted neighbors are selected
in the dialog.
¾ Press the icon to clear the selection.
6.5.4 Select Bonds by Type

¾ In the Bond Expression dialog, press Types.
All bond types are presented in the Bond Types dialog.
¾ Press ar then Add.
All aromatic carbons are highlighted, and the dialog reports that 6 bonds are
currently selected.
¾ Press the icon to clear the selection.
6.5.5 Select Bonds via Defined Sets

¾ In the Bond Expression dialog, press Sets.
The Sets for Bond Selection dialog presents named definitions that can be used
to identify bonds.
• A few built in sets can be applied to bonds. See Built-in Sets on page
223.
• Special purpose sets are defined in the macromol dictionary. See Global
Sets in the Biopolymer Dictionary on page 218.
Most defined sets pertain to biopolymers. However, one of them can be used as
an example for this tutorial: Rings.
¾ In the Built-in Sets section, activate Rings then press Add.
On the screen all ring atoms are highlighted. In the dialog the 19 bonds between
these atoms are selected.

¾ Press the icon.
This concludes the exercise about the Bond Expression dialog.
¾ Press Cancel to close the dialog.

How to Use the Substructure Expression Dialog
6.6 How to Use the Substructure Expression Dialog

Selecting a substructure can be done easily by double-clicking any of its atoms.
The purpose of this tutorial is to explore the functionality offered by the dialog.
A Matter of Time: This tutorial requires a couple of minutes of personal time.
6.6.1 Setup
1. Load crambin from a file in SYBYL’s demo directory.
¾ In the Open File dialog set the Files of Type to PDB.
¾ In the Selection list select 1crn.pdb then click OK.
2. Label the residues.
¾ Use on the View toolbar to label the substructures (Molecules >

Substructure).
3. Invoke a SYBYL feature that affects substructures.
¾ Biopolymer > Composition > Mutate Monomers
SYBYL opens the Sequence Expression dialog.
¾ If multiple molecules are currently on the screen, you must designate

the molecule area of interest at the top of the dialog.
6.6.2 Select Residues on the Screen

¾ Click on any atom of a single residue. The most reliable way to select
a particular residue is to select its alpha carbon, the atom bearing the
residue’s substructure label.
¾ To add to the selection, hold the Ctrl key while you click on another
residue.

Below the hierarchy in the dialog a line reports the number of substructures
currently selected.
¾ To clear the selection click anywhere on the SYBYL backdrop or

press the icon in the dialog.
6.6.3 Select Residues by Name in the Dialog

¾ In the Sequence Expression dialog, click and drag to select VAL8
through ASN12.
All atoms in the selected residues are highlighted in the display area. Below the
hierarchy in the dialog a line reports that 5 substructures are currently selected.
¾ Press the icon (Clear Selection).
6.6.4 Select Residues by Type

¾ In the Sequence Expression dialog, click Types to open the Residue
Types dialog.
The Residue Types dialog lists all possible monomer types available in the
dictionary. The standard amino acids are in the leftmost column. You can also
Sort Alphabetically to facilitate selection.
¾ In the Residue Types dialog, select CYS in the list and press Add.
The six CYS residues are highlighted with the green selection markers.
¾ Press the icon (Clear Selection).
6.6.5 Select Residues via Defined Sets

¾ In the Sequence Expression dialog, press Sets to open the Sets for
Substructure Selection dialog.
All sets in this dialog are substructure sets, which means that they apply to
entire residues. The list of sets is compiled from two sources:
• Special purpose sets whose definitions are stored in the macromol
dictionary. See Global Sets in the Biopolymer Dictionary on page 218.
• Sets that were created automatically by SYBYL upon reading the PDB
file. See sets created upon reading a PDB file (in the Biopolymer
Manual).
Selection based on conformational states, as defined in the dictionary, can also

be made in this dialog.

¾ Select HELIX_H1_PDB from the Sets list and press Add.
All atoms in residues in one of the two helices are highlighted with the green
selection markers.
This concludes the exercise about the Substructure Expression dialog.
¾ Press Cancel to close the dialog.

Chapter 7.
Clear and Reset the SYBYL Display
• Clear the Screen and Delete Objects on page 90

• Clear the Screen on page 90
• Delete Selected Molecules, Atoms and Backgrounds on page 90
• Delete Molecules on page 90
• Delete Atoms on page 91
• Delete Backgrounds on page 91
• Delete Whatever is Selected on page 92
• Reset Scaling, Translation, and Rotation on page 93

Chapter 7. Clear and Reset the SYBYL Display
Clear the Screen and Delete Objects
7.1 Clear the Screen and Delete Objects

The icon on the Edit toolbar consists of two buttons:
• Click the X to delete whatever is currently selected.
• Use the pull-down arrow to specify what will be deleted.
7.1.1 Clear the Screen

Delete absolutely everything in the SYBYL window.
Menubar: Edit > Delete Everything

Icon:
Click the icon’s arrow and select Delete Every-
thing.
Command Line: ZAP * to remove all molecules and associated back-
ground images followed by BACKGROUND DELETE * to
remove all remaining independent background images.
All molecules and all graphics images, known as backgrounds, are removed
from the SYBYL window.
7.1.2 Delete Selected Molecules, Atoms and Backgrounds

For information on how to select objects refer to:
Delete Molecules
Clear the molecule areas containing the selected molecules. This functionality is
enabled on the menubar and icon only if at least one atom has been selected.
Menubar: Select atom(s) in one or more molecules then

Edit > Delete > Selected Molecules
Icon: Select atom(s) in one or more molecules then
Click the icon’s arrow and select Selected Mol-
ecules.
Command Line: ZAP mol_expr

Background images, such as MOLCAD surfaces, associated with the deleted

molecules are removed from the screen as well.
Delete Atoms
Delete the selected atoms. This functionality is enabled on the menubar and
icon only if at least one atom has been selected.
Menubar: Select atom(s) in one or more molecules then

Edit > Delete > Selected Atoms
Icon: Select atom(s) in one or more molecules then
Click the icon’s arrow and select Selected
Atoms.
Command Line: REMOVE ATOM atom_expr
Issue this command for each molecule in which atoms
must be deleted, making sure to include the appropriate
molecule area within the atom expression.
See How to Specify an Atom Expression on page 203.
be deleted via this menu item or icon.
Unless entire molecules are deleted, the associated background images, such as
MOLCAD surfaces, remain on the screen.
See also Delete Atoms or Atom Attributes on page 121.
Delete Backgrounds
Delete one or more backgrounds. This functionality is enabled on the menubar

and icon only if at least one background is present.
A background is any graphics objects that is not a molecule. Examples are

MOLCAD surfaces and ribbons.
Menubar: Edit > Delete > Backgrounds (Surface, Ribbon,

etc.)
Select the background(s) to be deleted or ALL.
Icon:
Click the icon’s arrow and select Back-
grounds.
Select the background(s) to be deleted or ALL.

Command Line: BACKGROUND DELETE background_id

Specify the ID number of the background to be deleted
or * to delete all backgrounds at once. To find the ID
numbers of individual background images type LIST
BACKGROUND.
Background deletion cannot be undone.
Delete Whatever is Selected
Delete whatever is selected, atoms, surfaces or both. This functionality is

enabled on the menubar and icon only if at least one atom or surface has been
selected.
Menubar: Select atom(s) in one or more molecules and/or select

surface(s) then
Edit > Delete > Selected
Icon: Select atom(s) in one or more molecules and/or select
surface(s) then
Click to delete all selected objects.
If nothing had been selected before clicking the X,
nothing will be deleted.
Only atoms, MOLCAD surfaces and ribbons as well as potential surfaces can be
selected and deleted in this manner.
Read about The Selection Menu and Icons on page 63.

Reset Scaling, Translation, and Rotation
7.2 Reset Scaling, Translation, and Rotation

7.2.1 Reset All
Reset SYBYL’s graphics window to the original scale, rotation, and translation
settings.
Menubar: View > Transformations > Reset All

Icon:
Click on the View toolbar.
7.2.2 Reset Selectively

Reset all or selective scale, rotation, and translation settings.
Icon:
Use on the Miscellaneous toolbar.
Command Line: STATIC RESET

Undo the Last Operation
7.3 Undo the Last Operation

Each molecule area has a single level stack associated with it. Prior to an
operation that affects a molecule’s coordinates, or atom and bond definitions,
the current state is saved on this stack. If you choose to reverse the action of a
command, this data is available to return to the previous state.
Menubar: Not accessible from the menubar.

Command Line: RECOVER mol_area
UNDO (identical to RECOVER M*)
Notes:
1. The state saved to the stack includes coordinates, atom and bond definitions.
2. UNDO and RECOVER do not reverse the effect of labels or colors.
• If you want to reverse the effect of a labeling operation, use View >
Unlabel.
• You can not reverse the effect of coloring operations. If you have a color
scheme you wish to save, you need to save the molecule with that color
scheme.
3. The automatic saving to the stack is controlled by the SET AUTOSAVE
command (described in the Graphics Manual).

Chapter 8.
Build and Modify Molecules
Use the options under the Edit menu (described in Menubar to Command
Mapping) to sketch and modify molecules. Use the Sketch Molecule menu
option to draw a molecule. The other menu options allow you to add, define,
modify, copy, and delete various molecular components.
• Sketch a Small Molecule Tutorial on page 96
• Ring Fusion Tutorial on page 103
• Load Fragments on page 109
• Access the Sketcher on page 111
• Sketching Techniques on page 111
• Sketcher Toolbars on page 115
• Modify Molecules Outside of the Sketcher on page 118
• Atoms on page 118
• Bonds on page 125
• Chemical Group on page 128
• Delete or Modify Substructures on page 129
• Chirality on page 130
• Center of Rotation, Name, Type, etc. of a Molecule on page 133
• Combine (Fuse) Two Molecules on page 134
• Adjust Bond Lengths and Angles to Match Standards on page 135
• Scan Torsions to Reduce van der Waals Contacts on page 136
• Create a Molecule by Averaging Existing Molecules on page 136
• Define and Modify Geometric Features on page 138

Chapter 8. Build and Modify Molecules
Sketch a Small Molecule Tutorial
8.1 Sketch a Small Molecule Tutorial

This tutorial introduces the most common features of SYBYL’s sketcher. See
Sketcher Toolbars on page 115 for a full description.
8.1.1 Preface
In this tutorial, you will build and minimize Atropine by building the most
complex ring system first and then adding the substituents. Typically, molecular
fragments from the Standard Fragment Library are used to quickly construct
ring systems with good geometry. However, in order to better demonstrate
SYBYL’s sketching capabilities, you will use the Sketch Molecule menu
items to construct and optimize the most complex ring system.
After completing this tutorial, you will be able to:

• Draw a ring
• Draw a chain
• Add substituent groups
• Check and assign chirality
Before performing the following tutorial you should be familiar with the
graphics functions of SYBYL. If necessary, refer to the Quick Reference
section in the Graphics Manual for a summary.

8.1.2 Set Up
1. It is always a good idea to clear the screen and reset the display before starting.
¾ Use on the Display toolbar to set the screen mode to Full.
2. Adjust the tailor setting for cleaning up structures within the sketcher.
¾ Options > Tailor
¾ In the Tailor dialog, set the Subject to SKETCH.
¾ Set the CLEAN_UP option to 6_MINIMIZE
The default is 4_SCAN, which involves non ring bonds only. For this example,
the ring systems need to be cleaned up as well and using 6_MINIMIZE will
accomplish this by doing an energy minimization of the sketched structure.
Any clean up option from 2 to 6 includes all options preceding it in the list,
therefore, all non-ring bonds have their bond lengths and angles adjusted, and
the torsion angles are scanned and adjusted to relieve bad contacts.
¾ Press Apply then Close.
8.1.3 Enter the Sketching Mode

1. Display the sketch menus and select M1 as the work area in which to build the
molecule.
¾ File > New > Small Molecule
A series of toolbars are added to the SYBYL window. You may reposition them
along any edge of the SYBYL window. See Sketcher Toolbars on page 115 for
a full description.
You are automatically placed in Draw mode, as indicated by , so you can

begin sketching immediately.
2. Display a grid to aid in building the molecule to scale. The spacing between
grid points is 1.54 Å, the sp3 carbon to sp3 carbon bond length. The grid scales
with the molecule in order to show the correct bond length.
¾ Click to display the grid.

Note: If the grid gets in your way, toggle it off by pressing again.
8.1.4 Sketch the Ring System

1. Build the piperidine ring as follows:
¾ Click in the middle of the screen.
SYBYL displays a “+” representing an unconnected atom. The small box

around it indicates that this atom is the current attachment point to which the
next sketched atom will be attached.
¾ Click a point above the first atom and approximately one grid spacing
to the right (see atom 2 in the figure below).
SYBYL draws a bond to the newly created second atom.
¾ Continue sketching the 6-membered ring by clicking appropriate

points on the screen.
¾ Close the ring by selecting atom 1 again.
When you close the ring by picking atom 1, no atom is highlighted, indicating
that continuous Draw mode is temporarily deactivated. Continuous mode is
always suspended when an existing atom is chosen, whether it is the current
atom of attachment or another atom. In the former case, no bond is drawn; while
in the latter case, a bond is drawn and then continuous draw mode is deacti-
vated.
2. Change the type of atom 1 to a nitrogen.

¾ On the second toolbar (showing various atomic symbols), click N.
¾ On the first toolbar, click .
¾ Click atom 1 on the sketched molecule.
SYBYL displays a label indicating that the type has been successfully changed
and the atom is colored blue.

3. Introduce a third dimension to the molecule.
¾ Click and hold down the Left mouse button and drag the cursor up to
rotate the molecule about the X axis until it has an orientation similar
to that shown in the figure below.
4. Add the bridge across the ring.
¾ On the second toolbar, click C then click to go back to draw

mode.
¾ Click atom 2 to make it the current attachment atom.
¾ Click a point below atom 2 and then another point diagonal to the
new atom.
¾ Click atom 6 to close the ring.
5. Move carbon 4 down to give the ring a chair conformation.
¾ Click , then on atom 4 then on a point below it and below the

plane of the ring.
6. Clean up the ring system.
¾ On the first toolbar, click .
The molecule’s geometry is optimized quickly using the Tripos force field.

8.1.5 Add a Chain

1. Center the molecule on the screen.
¾ Click to center the molecule.
¾ Rotate the molecule until its orientation is similar to that shown in the
figure below.
2. Add a carbon chain to the ring.
¾ Click atom 4 as the new attachment atom.
¾ Sketch the chain by clicking successive points at approximate

locations on the screen for atoms 9 through 13.
¾ Click atom 13 again to deactivate continuous Draw mode and end the
chain.
3. Draw a double bond for the carbonyl group.

¾ Click atom 10 as the new point of attachment and then click a point
above the atom.
¾ Click atom 10 again.
The double bond appears and continuous Draw mode is deactivated, since an
existing atom was chosen.
4. Add a carbon to the nitrogen.
¾ Click atom 1 (N), then a point to its left.
¾ Click that new atom again to deactivate continuous Draw mode.
5. Sketch the ester and hydroxyl groups.
¾ On the second toolbar, click O then click .

¾ Click each of the three atoms: 9, 13, and the end of the double-bond.
The atoms are labeled with an O and colored red to reflect the change.
8.1.6 Add a Phenyl Group

1. Add a phenyl ring to the molecule.
¾ On the third toolbar (showing various groups), click PHENYL.
¾ In the structure, click atom 11.
2. Center the molecule.
¾ Click .
¾ Compare your sketch with atropine.
8.1.7 Check the Chirality

Make sure that atom 11 has a chirality of S.
¾ Click and click atom 11.
¾ In the console type S and press the Enter key.
If atom 11 is already an S chiral center, a message is displayed in the console

informing you of this and nothing else happens. If, however, the R chiral center
has been sketched, the center is inverted to assume the proper stereochemistry.

8.1.8 Clean Up the Model

1. Clean up the model.
¾ Click .
2. Add the necessary hydrogens to all unfilled valences.
¾ Click to fill all open valences with hydrogens.
All atom and bond types are automatically converted to SYBYL types, based on
the connectivity prior to adding hydrogens.
3. Exit the sketching mode.

¾ On the first toolbar click EXIT.
A final clean up is done automatically when you exit the sketcher.
8.1.9 Save the Sketched Molecule

1. Name the molecule.
¾ Click on any atom then Edit > Molecule > Name
¾ Type atropine and press OK.
2. Save the full description of the molecule in a text file.
¾ In the Save Molecule dialog, by default, atropine appears in the File

field.
¾ By default, the Format is set to MOL2.
¾ Press Save.
A file named atropine.mol2 is created in the current directory.
3. This concludes the small molecule sketching tutorial.
In this tutorial, you built and minimized atropine by building the most complex
ring system first and then adding the substituents.

Ring Fusion Tutorial
8.2 Ring Fusion Tutorial

The following tutorial illustrates several examples of fusions:
• Fuse Two Planar Bonds
• Fuse Two Rings to Build a Spiro System
• Fuse Two Non Planar Bonds
• Fuse A Planar Bond With A Non Planar Bond
8.2.1 Set Up
8.2.2 Fuse Two Planar Bonds

The fusion of two planar systems requires only two pair of atoms. In this
example, furan (M1) is fused to pyridine (M2) and the resulting model appears
in M2.
1. Read in the two fragments, color them by atom type, and label both structures.
¾ Select FURAN and press OK.
¾ Select PYRIDINE and press OK.
2. Set the Screen mode to display the molecules side by side.
¾ Use on the Display toolbar to set the screen mode to Half.
3. Label the atoms by ID numbers.
¾ Use on the View toolbar to label the Molecules by Atom ID.

4. Fuse the two structures.
¾ In the console, type: fuse
¾ Click atom 6 in pyridine, and then atom 2 in furan to form the first
pair.
¾ Click atom 5 in pyridine, and then atom 3 in furan to form another
pair.
¾ In the Select Atom dialog, press End.
Furan is fused to pyridine. The molecule whose atom was selected first
(pyridine) to perform the ring fusion is updated.
8.2.3 Fuse Two Rings to Build a Spiro System

You can specify a spiro fusion by first selecting the two atoms that become the
spiro center. The second pair involves a ring atom in one molecule and a
hydrogen in the other.
1. Clear the SYBYL screen.
2. Read in the two molecules.

¾ Select 4H-PYRAN and press OK.
¾ Select PIPERIDINE and press OK.
3. Label the atoms by ID numbers.
¾ Use to label the Molecules by Atom ID.
4. Fuse the two rings.
¾ Click atom 4 in piperidine, and then atom 4 in 4H-pyran to form the

first pair.
¾ Click atom 12 in piperidine, and then atom 5 in 4H-pyran to form
another pair.

The two rings are fused with a spiro center; the resulting model appears in M2.
8.2.4 Fuse Two Non Planar Bonds

In the following steps, you will fuse tetrahydropyran (M1) to piperidine. Several
methods are used by providing:
• Two pair of atoms (result in M2),
• Three pair of atoms (result in M3),
• Four pair of atoms (result in M4).
1. Clear the SYBYL screen.
2. Load the molecules and label the atoms.
¾ Select TETRAHYDROPYRAN and press OK.
¾ Select PIPERIDINE and press OK.
¾ Use to set the screen mode to Quartered.
¾ Double-click any atom in piperidine to select the entire molecule.
¾ Edit > Copy (or click on the Edit toolbar).
¾ Select M3:<empty> and press OK.
¾ Click , and press OK to accept M4:<empty> as the destination.
¾ Click away from all molecules to clear the selection.
3. Use two pair of atoms to fuse two non planar bonds. SYBYL resolves the
ambiguity automatically by selecting the alternative which gives rise to the best
fusion geometry. The results are displayed in M2.

¾ Click atom 6 in piperidine (in M2), and then atom 3 in tetrahydropyran

to form the first pair.
¾ Click atom 5 in piperidine (in M2), and then atom 2 in tetrahydropyran
to form another pair.
Two non planar bonds are fused. The resulting model with extraneous
hydrogens appears in M2, showing that the selection of two atom pairs was
insufficient for this type of fusion.
4. Use three pair of atoms to fuse two non planar bonds. As in the previous steps,
SYBYL automatically resolves the ambiguity. The results are displayed in M3.
¾ Click atom 6 in piperidine (M3), and then atom 2 in tetrahydropyran

(M1) to form the first pair.
(M1) to form a pair.
Two non planar bonds are fused; the resulting model appears in M3.
5. Use four pair of atoms to fuse two non planar bonds. The results of the fusion
are displayed in M4.
Manual fitting of the two bonds to be fused reveals that the torsional angles of
the four atoms involved are 60° in piperidine and -60° in tetrahydropyran. In
order to produce a geometry better suited for the cis fusion you want to perform,
tetrahydrofuran is inverted first.
¾ Edit > Chirality > Invert
¾ Select M1:tetrayhydropyran from the pull-down.
¾ Press the icon and press OK.
¾ Clear the atom selection.


Two non planar bonds are fused; the resulting model appears in M4.
8.2.5 Fuse A Planar Bond With A Non Planar Bond

1. Load the molecules and label the atoms.
¾ Select HEXAHYDROAZEPINE and press OK.
¾ Select BENZENE and press OK.
¾ Use to set the screen mode to Half.
2. Fuse benzene (M2) to hexahydroazepine (M1) to form a model in M1.
¾ Click atom 5 in hexahydroazepine (M1), and then atom 1 in benzene

¾ Click atom 4 in hexahydroazepine (M1), and then atom 2 in benzene

The planar bond is fused with a non planar bond. Notice the poor quality of the
geometry at the ring fusion and the fact that extraneous hydrogens are left over
from the hexahydroazepine. Clean up and minimization are necessary before
this model could be used.
The best strategy to assure the quality of the fusion and reduce the need for
minimization is to make sure that the geometry of the bonds to be fused is
identical in both molecules before the fusion occurs.
3. Set the Screen mode to full.
¾ Use to reset all rotations and translations.
¾ Use to reset the screen mode to Full.
This concludes the Ring Fusion Tutorial.

Load Fragments
8.3 Load Fragments

SYBYL provides a library of fragments from which you can easily build most
molecules. The following table describes information for using the menubar or
command line to select and display fragments contained in the Fragment
Library.
Menubar: File > Get Fragment

• Select one fragment in the list.
The fragment will be loaded into the first empty mole-
cule area.
Use the Fragment FRAGMENT MENU menu_choices mol_area
Library search • menu_choices—Series of numbers, typed at the
menu via Com- keyboard, identifying successive menu items.
mand Line: • mol_area—Area to receive selected fragment,
current contents are overwritten.
Menus are hierarchical and categorize various molecu-
lar fragments according to structure and/or function.
The DATABASE SEARCH command, for example, uses a
menu structure to control searching of a database. Enter
number of menu items to move up or down the hierar-
chy until desired molecule is found. Typing the num-
ber of an actual molecule retrieves that molecule.
There are also three words that are valid choices:
• TOP—Return to top level of menu hierarchy, where
the most general categories are displayed.
• UP—Back up one level in the hierarchy to a set of
more general categories.
• QUIT—Exit from search procedure without
choosing a molecule.
Load a Single FRAGMENT NAME name [mol_area]
Fragment by name • name—Name (with optional wildcards) of fragment
via Command to retrieve.
Line: • mol_area—Area to receive the fragment.
For example, FRAGMENT NAME BENZENE M1 retrieves
the fragment BENZENE into M1.
FRAGMENT NAME VIT*B2 M1 retrieves the fragment
Vitamin B2 into M1 (because only one fragment satis-
fies the expression VIT*B2).

Load Fragments
Load Multiple FRAGMENT NAME name_expr

Fragments from [QUIT|RETRIEVE|SELECT|UNSELECT]
Library via Com- • name_expr—Name (with optional wildcards) speci-
mand Line: fying multiple fragments to retrieve.
If no fragment is found or if single fragment is
retrieved, no further input necessary (i.e., entering one
of the following items is skipped).
• QUIT—Exit search procedure without choosing a
molecule.
• RETRIEVE [mol_area]—Retrieve multiple
fragments starting with specified mol_area.
• SELECT [name_expr]—Select subset of currently
chosen molecules according to their names.
• UNSELECT—Unselect list of fragments. This undoes
previous SELECT operation, thus allowing a more
flexible search of the library. It can be applied any
number of times.
For example, FRAGMENT NAME BE* RETRIEVE M1
retrieves all fragments starting with the letters BE and
places them in consecutive molecule areas starting with
M1.
• Libraries of Chemical Groups and Fragments on page 231.
• Load a Molecule from the Fragment Library: on page 16 for an example
exercise.

Access the Sketcher
8.4 Access the Sketcher

Menubar: File > New > Small Molecule
or Edit > Molecule > Sketch
See Sketcher Toolbars on page 115.
Toolbar Icon:
on the Molecule toolbar.
Command Line: SKETCH mol_area
File > New > Small Molecule always uses the first empty molecule area.
Edit > Molecule > Sketch and determine the molecule area to use as
follows:
• If nothing is selected, the Sketcher uses the first empty molecule area.
• If one or more atoms are selected in the same molecule area, the
Sketcher is launched for that molecule area. This is how to use the
Sketcher to modify an existing molecule.
• If atoms were selected in multiple molecule areas you will be prompted
to specify which molecule area the Sketcher will operate on.
• Additionally, any hidden atoms in the selected molecule are made
visible upon invoking the Sketcher.
Molecules are drawn flat until you rotate the structure. Any atom added subse-
quent to a rotation assumes the transformed Z-coordinate of the atom to which it
is bonded. Unconnected atoms are always two-dimensional since there is no
reference point.
• Sketching Techniques on page 111
• Edit > Clean-Up Molecule > 3D Geometry (Concord) for fast
conversion of 2D coordinates to 3D (in the Concord Manual).
• TAILOR SET GRID to customize the displayed grid.
8.4.1 Sketching Techniques

The following sections discuss some basic ideas and helpful techniques for
using the Sketcher.
You can start sketching with an atom or a fragment.
Important: You can not start sketching with a chemical group.

Access the Sketcher
Always Review the Sketched Model
Although flexible enough to enable building any structure, the Sketcher does
have enough chemical sense to warn you when you have done something
unnatural. For example, SYBYL displays a message if the valence of an atom is
about to be exceeded. It is your decision to continue or not.
About Continuous Drawing Mode
You can stop the continuous drawing mode (also referred to as “pen up
movement”) by doing one of the following:
• To cancel the selection of a point of attachment, click the last atom
drawn.
You can then move the cursor to another part of the molecule without
drawing a bond. When you pick a new point of attachment, continuous
drawing mode is turned on again.
• Click an existing atom. A bond is drawn from the current atom to this
existing atom and then the pen up movement is initiated.
Atomic Symbols Only
SYBYL designates the atom types with only the atomic symbols, in order to
eliminate the burden of having to decide the proper SYBYL atom type.
Atom Types
You can change the atom types in two different ways:
Method One: Change the default atom type, before adding the new atom to the
model:
1. On the second toolbar, click the desired atomic symbol.
If the atom type is not listed, click More to display a periodic table and
select the desired atomic symbol. The table is color-coded using the SYBYL
atom type coloring scheme. Once a selection is made, click X in the upper
corner to close the table. (Note that the selected atomic symbol now appears
as a button below the More button in the toolbar.)
2. Click in the display area to add a new atom of that type.
Subsequent atoms have the new atom type until you select a different atomic
symbol. Use this technique if you want to draw a chain of atoms, other than
carbons.

Access the Sketcher
Method Two: Modify the type of an existing atom:

1. On the second toolbar, click the desired atomic symbol.
If the atom type is not listed, click More to display a periodic table and
select the desired atomic symbol. The table is color-coded using the SYBYL
atom type coloring scheme. Once a selection is made, click X in the upper
corner to close the table. (Note that the selected atomic symbol now appears
as a button below the More button in the toolbar.)
2. On the first toolbar, click .
3. Click the atom whose type you want to change.
SYBYL updates the atom type.
Branching
To draw an atom not connected to the last atom displayed, a pen up action must
be signified by choosing this last (highlighted) atom again. SYBYL removes the
highlighting and temporarily turns off the continuous draw mode. When you
choose a new point of attachment, SYBYL automatically turns the continuous
drawing mode on and you can add a new chain of atoms.
If you select a point of attachment in error, click that atom again to initiate the
pen up movement. You can now select a new point of attachment.
Edit Existing Molecules
Existing molecules or fragments can be brought into the sketcher in order to

make quick modifications. When the sketcher is exited or the clean-up option
selected, only the part of the molecule that changed is cleaned up. The rest of
the molecule maintains its current geometry. You can disable this option by
setting TAILOR SET SKETCH AGGREGATES to OFF. With this option, the
whole molecule is considered in the clean up phase.
Label and Color
In order to make different atom types easily identified, heteroatom labeling and
molecule color, coded by atom type, are the sketcher defaults.
Multiple Bonds
Draw the single bond, then do one of the following:

• If the last atom drawn is one of the atoms involved in the double bond,
select the target atom and a second line appears between the two atoms
designating the double bond. Since the target atom is an existing atom,

Access the Sketcher
continuous drawing mode is temporarily turned Off and a new point of

attachment must be chosen before drawing commences again.
• If neither atom defining the double bond is currently selected, turn Off
continuous drawing mode by picking the last atom drawn a second time.
Select one of the atoms of interest as the new point of attachment. Pick
the target atom for the double bond and a double line appears between
the two atoms. As mentioned above, since the target atom is an existing
atom, drawing mode is temporarily suspended.
The same strategy can be repeated for sketching triple bonds. Aromatic bonds
are designated by alternating single and double bonds within the ring.
Rings
Sketch the backbone on the ring by picking points at appropriate positions on

the screen. To close the ring select the first atom of the ring again, thereby
causing a bond to be drawn between this atom and the last atom drawn. Since
this ring closure atom is an existing atom, SYBYL temporarily stops the
continuous draw mode, so you can choose a new point of attachment. To add a
bond to the current atom, select that atom again.
Z Coordinate
To add a third dimension to the molecule, apply rotations to the model. Once an
atom has a Z-coordinate, any subsequent atoms attached to it are drawn in the
same Z-plane. For example, if a rotation precedes moving an atom ( ), the
atom being moved is drawn in a different plane from the rest of the molecule.
Many different conformations of a molecule can be achieved with this method,
such as chair or boat cyclohexane.

Access the Sketcher
8.4.2 Sketcher Toolbars

Accesses:
• File > New > Small Molecule
• Edit > Molecule > Sketch
• on the Molecule toolbar.
Usage Notes:
• To build upon a chemical fragment you must retrieve the fragment
before accessing the Sketcher. See Load Fragments on page 109.
• The clean up method to be used when exiting the Sketcher must
specified before accessing the Sketcher. See TAILOR SET SKETCH
CLEAN_UP in the Tailor Manual. The default method (4_SCAN) fixes
non-cyclic bond lengths and valences angles and rotates non-cyclic
bonds to escape atomic overlaps.
The Sketcher has 3 toolbars of icons grouped as follows:

• Sketching Functions — Activities necessary to sketch a structure. See
Sketching Functions Toolbar below for descriptions.
• Atomic Symbols — Pick one of these atomic symbols to indicate the
atom type to draw. If the atom type is not listed, click More to display a
periodic table and select the desired atomic symbol. The table is color-
coded using the SYBYL atom type coloring scheme. Once a selection is
made, click X in the upper corner to close the table. (Note that the
selected atomic symbol now appears as a button below the More button
in the toolbar.)
• Groups — Substructures defined in the Group Library. Groups have
predefined attachment points. (Refer to Group Library Structure and
Contents on page 232 for more information.)
Usage Note: you cannot start sketching with a chemical group. An atom
must exist as an attachment point before a functional group can be
added.
A toolbar can be moved to the top or the right side of the display area by
clicking on the dashed line and dragging it to the new location.
Toolbars can be reordered by dragging one at a time to the last position (closest
to the display area). You can also combine toolbars by dragging one over the
other. (This is what always occurs if you move more than one toolbar to the top
of the display area.)

Access the Sketcher
Sketching Functions Toolbar
Activates the continuous drawing mode, the default action,

with the cursor defined as a carbon atom.
To draw a chain of carbons:
• Click a point on the screen where the first atom is to be
located; a cross appears.
• Click another point on the screen; that point appears
and SYBYL draws a line (bond) between the two
atoms.
• Continue clicking until you reach the desired chain.
Note that the current atom of attachment is always high-
lighted.
Places you in modify mode. Clicked atoms are replaced by
the atom selected in the second toolbar.
Prompts you for the atom to move and its new location.
The atom, and all bonds connected to it, are moved to the
new location. This mode remains active until you select
another option. This capability is useful when building a
particular conformer.
Deletes the current sketch molecule.
Removes a bond from the drawn structure. You must

select two bonded atoms.
Undoes the last operation, restoring the molecule to its
previous state. Note: If you want to reverse the effect of
the LABEL command, use UNLABEL.
Centers the molecule on the screen.
Adjusts molecule geometry according to the method speci-

fied via the TAILOR SET SKETCH CLEAN_UP command.
Also determines the proper atom hybridization, based
upon bond type and atom type of connected atoms. No
matter which option is chosen for clean-up, the atom and
bond type conversion is always done.
Adds hydrogens to all unfilled valences.
Removes all hydrogens in the sketched molecule.
Deletes atoms, and any bonds connected to them, from the

molecule being sketched. This mode remains active until
you select another option.
Specifies whether a chiral center is R or S.

Access the Sketcher
Modifies the torsion angle of four connected atoms.
Modifies the bond angle of three connected atoms.
Toggles the grid on and off. Use the grid to aid sketching.
Spacing between grid points is 1.54 Å, the approximate
length of a carbon-carbon single bond.
EXIT Performs clean up procedure and assigns SYBYL atom
types (see description for the clean up tool).

Modify Molecules Outside of the Sketcher
8.5 Modify Molecules Outside of the Sketcher

• Atoms on page 118
• Bonds on page 125
• Chemical Group on page 128
• Delete or Modify Substructures on page 129
• Chirality on page 130
• Center of Rotation, Name, Type, etc. of a Molecule on page 133
• Adjust Bond Lengths and Angles to Match Standards on page 135
• Scan Torsions to Reduce van der Waals Contacts on page 136
• Create a Molecule by Averaging Existing Molecules on page 136
8.5.1 Atoms
Add an Atom to an Existing Structure
Menubar: Edit > Atom > Add Connected Atom

Command Line: ADD ATOM attachment_atom type
• attachment_atom—Atom to which new one is bonded.
• type—New atom’s chemical type and hybridization.
(Type “?” at prompt to list available atom types.)
SYBYL automatically determines the coordinates, based on bond length and

bond angle data from parameter tables.
Add a Standalone Atom
Menubar: Edit > Atom > Add Standalone Atom

Command Line: ADD RAWATOM mol_area name type x y z
• mol_area—Area to receive new atom.
• name—Name for new atom (must start with an alpha-
betic character and contain only alphabetic characters,
digits, and/or the special symbols dollar sign ($), under-
score (_), or apostrophe (')).
• type—Chemical type and hybridization of atom. (Type
“?” at prompt to list available atom types.)
• x, y, z—Coordinates of atom.

Position the atom by specifying coordinates or by using the mouse.
Add a Chain of Atoms of the Same Type
Menubar: Edit > Atom > Add Chain of Atoms

Command Line: ADD CHAIN ATTACH | REPLACE [atom] type
length
• ATTACH—Add new chain to specified atom with appro-
priate geometry.
• REPLACE—Remove specified atom and add new chain
in its place, with ideal geometry (useful when
hydrogens are present).
• atom—Atom for attachment or to replace.
• type—Chemical type and hybridization of atoms in
chain. (Type “?” at prompt to list available atom types.)
• length—Length of chain to create, may vary from 1
upward (no upper limit). “1” is equivalent to the ADD
ATOM command.
SYBYL attaches chains to the existing structure with ideal geometry. SYBYL
determines the coordinates of all atoms from the parameter tables.
Add Pseudo-atoms (Centroids)
Pseudo-atoms (centroids) are added to prochiral, methyl, and phenyl ring

groups. They are often used for defining constraints to the prochiral, methyl, or
aromatic protons. Constraints are needed when you do not have stereospecific
resonance assignments for prochiral atoms (or methyl pairs, such as in leucine
and valine), or when fast motions are present (such as methyl rotors and
aromatic ring flipping).
Menubar: Edit > Atom > Add Pseudo-atoms

Command Line: ADD_PSEUDOATOMS mol_area
The dummy atom’s name at the centroid position is defined according to the
nomenclature first presented in Kurt Wüthrich, NMR of Proteins and Nucleic
Acids, J. Wiley and Sons, 1986. For example, the beta methyl group on alanine
is named “QB”.
The algorithm identifies appropriate atom sets, independently of the

substructure and atom names. For example, any pair of protons bonded to a
“heavy” atom, and that are not part of methyl groups, will have a pseudo-atom
added between them.

Add Hydrogens
Fill all empty valences with hydrogens. If the molecule is a protein, nucleic
acid, or saccharide, the Biopolymer functionality, BIOPOLYMER ADDH, is
exercised first. See License Requirements for SYBYL Basics on page 8.
Hydrogens added to invisible atoms are automatically made invisible.
Menubar: Edit > Hydrogens > Add All Hydrogens

Edit > Hydrogens > Add Polar Hydrogens
Edit > Hydrogens > Add Non-Polar Hydrogens
Adding hydrogens works on whole molecule areas, affect-
ing only those containing selected atoms or all of them is
nothing is selected.
The {POSSIBLE_HBOND} built-in set is used to identify
polar hydrogens.
Icon:
on the Display toolbar. Add all hydrogens to molecule
areas containing selected atoms or to all of them if nothing
is selected.
Command Line: FILLVALENCE atom_expr H
• atom_expr—Atoms to have empty valences filled with
hydrogens.
SYBYL sets bond lengths and angles to standard values determined from the
parameter file (described in the Force Field Manual).
Hydrogens, when added, acquire the rendering mode of the atoms they are
attached to.
Fill Empty Valences with any Atom Type

Command Line: FILLVALENCE atom_expr atom_type
• atom_expr—Atoms to have empty valences filled.
• atom_type—Mnemonic type of atom to use in filling
valences.
SYBYL sets bond lengths and angles to standard values determined from the
parameter file.

Delete Atoms or Atom Attributes
Delete All Hydrogens:
Edit > Hydrogens > Delete All Hydrogens
Deleting all hydrogens works on whole molecule areas, affecting only those
containing selected atoms or all of them is nothing is selected.
Delete Selected Atoms:

Menubar and toolbar require pre-selection of atoms.
Menubar: Edit > Delete > Selected Atoms

Toolbar:
> Selected Atoms
Command Line: REMOVE ATOM atom_expr
Deleting atoms also removes all bonds involving the deleted atom(s) and any
features (normal, plane, constraint) attached to them. SYBYL renumbers atoms
and bonds to reflect the removal of objects from the molecular description. If
the removed atom is a member of a static set, the set membership is updated.
Removing all atoms is equivalent to deleting the molecule.
Delete a Connected Group of Atoms:
Use the Split functionality to remove a portion of a molecule by specifying two

bonded atoms:

Command Line: SPLIT origin_atom target_atom
SYBYL deletes the bond between the specified atoms along with all atoms on
the target side of that bond.
Note: You can not use the Split functionality if the indicated bond is in a ring.
You must first break the ring by removing a bond or an atom.
Delete Atom Attributes:

Attributes can be removed from one or more atoms without deleting the atom
itself.
Command Line: REMOVE ALL_ATOM_ATTRS atom_expr

Modify an Atom
Menubar: Edit > Atom > Modify

Change Point MODIFY ATOM CHARGE atom_expr charge
Charge via Com-
mand Line:
Change Coordi- MODIFY ATOM COORDINATES atom_expr
nates: xyz_coord
Changes are not restricted by the bond length table nor
by atoms being in rings. Coordinates are unconditionally
altered.
Update Lone Pairs: MODIFY ATOM LONE_PAIR atom_expr
Lone pair positions may need to be updated after whole
or partial structural changes are made to the molecule,
such as minimizations. Geometry optimizations using
Tripos force field do not affect lone pair positions. Use
this command before defining an extension point if any
atoms involved are lone pairs.
Change Name: MODIFY ATOM NAME atom_expr
APPEND_AUTO|QUERY|SEQUENTIAL_AUTO
• APPEND_AUTO—Supply a single string to concate-
nated with current name for each selected atom.
• QUERY—Prompts for name for each selected atom.
• SEQUENTIAL_AUTO—For each selected atom,
concatenate name of atomic element with the atom
ID number to form new name.
First character of name must be alphabetic. All others
must be alphabetic, numeric, or the apostrophe.
Change Only Type MODIFY ATOM ONLY_TYPE atom_expr {type}
(not Geometry): Prompts for the type for each specified atom. SYBYL
modifies the types of bonds associated with the atoms to
fit the new atom types.
The geometry around atoms or atom names is not
changed. TAILOR SET ATOM_TYPE FIX_NAMES sets
whether atom names are affected by changes to an
atom’s type.
Recalculate Exten- MODIFY ATOM SYBYL_POINTS atom_expr
sion Points/Lone Use if extension points/lone pairs become distorted dur-
Pairs: ing other calculations.

Change Type and MODIFY ATOM TYPE atom_expr {type}

Geometry: Prompts for the type for each specified atom. After all
new types have been entered, SYBYL modifies the
types of associated bonds to fit the new atom types. For
non-ring atoms, SYBYL also adjusts bond lengths.
Bond lengths and types are taken from
$TA_ASCTABLES/BOND_LENGTHS and
BOND_TYPES. If the bond type is ambiguous (i.e., there
is more than one possible bond type to connect the two
atom types) or unknown, you are prompted.
You can rename atoms by preserving the suffix and
replacing the old atomic symbol with the new one. This
prevents situations such as replacing a carbon labeled
C8 with a nitrogen, and the label is still C8. TAILOR
SET ATOM_TYPE FIX_NAMES sets whether atom names
are affected by changes to an atom’s type.
Assign Alternate MODIFY ATOM OTHER_TYPES set_name ASSIGN
Types SPECIFIC|UNKNOWN
• set_name—Set of alternate atom types: KOLL_ALL,
KOLL_UNI, AMBER7_FF02, AMBER7_FF99,
AMBER95_ALL, or MMFF94.
• SPECIFIC—Specify atoms to assign types to. You
are prompted for the atom types, one at a time, as the
atom is highlighted.
• UNKNOWN—Prompts for atom types for each atom in
molecule which does not have an alternate atom
type.
Licensing: See License Requirements for SYBYL
Basics on page 8.
Assign Alternate MODIFY ATOM OTHER_TYPES set_name
Type via SLN SLN_AUTO_ASSIGN SPECIFIC|UNKNOWN
AMBER7_FF02, AMBER7_FF99, AMBER95_ALL.
• SPECIFIC—Specify atoms to assign types to.
• UNKNOWN
Unassign Alter- MODIFY ATOM OTHER_TYPES set_name UNASSIGN
nate Types atom_expr
SYBYL will use the default (dictionary) value for the
alternate atom type instead of user-assigned value.

Label Alternate MODIFY ATOM OTHER_TYPES set_name LABEL

Types mol_area
Menubar: View > Label > Molecules > Atom Type
(applies to pre-selected atoms or to all molecule areas if
no atoms were selected). See Label in the Graphics
Manual.
Licensing: See License Requirements for SYBYL
Basics on page 8.
Unlabel Alternate MODIFY ATOM OTHER_TYPES set_name UNLABEL
Types mol_area
List Alternate MODIFY ATOM OTHER_TYPES set_name LIST SPE-
Types CIFIC|UNKNOWN|USER_ASSIGNED
• SPECIFIC—List alternate types of all specified
atoms, including source of alternate type (user-
specified, or default—from macromol dictionary).
• UNKNOWN—List names of all atoms with unknown
alternate atom types.
• USER_ASSIGNED—List types of all atoms with user-
assigned alternate types.
Alternate atom types can come from two sources: the macromol dictionary (also
referred to as the default source) or user input. Alternate atom types are needed
for energy calculations using non-Tripos force fields. MODIFY ATOM
OTHER_TYPES displays or lists alternate atom types from either source, and
allows input of user-assigned alternate types. User-assigned types are stored
with the molecule, and take precedence in force field calculations over
dictionary-supplied alternate atom types. Currently supported alternate atom
type sets are:
• Kollman all-atom (KOLL_ALL) and Kollman united-atom (KOLL_UNI)
force fields. A list of Kollman atom types is provided in the Force Field
Manual. Note: Alternate atom types must be defined for both KOLL_UNI
and KOLL_ALL force fields for energy setup to work. If the atom type is
defined for only one, the ENERGY, MAXIMIN2, and DYNAMICS SETUP
commands all fail with an error condition.

• AMBER7 FF99 (AMBER7_FF99) force field, which is essentially

AMBER95 atom types with a few types added. A list of AMBER7 FF99
atom types is provided in the Force Field Manual.
• AMBER7 FF02 (AMBER7_FF02) force field, which is essentially
AMBER7 FF99 atom types with different charges and polarization
included. A list of AMBER7 FF99 atom types is provided in the Force
Field Manual.
• AMBER 95 (AMBER95_ALL) force field.
• MMFF94 force field. A list of MMFF94 atom types is provided in the
Force Field Manual.
• The Load Charges section of the Biopolymer Manual to load atomic
charges and alternate atom types from the dictionary.
8.5.2 Bonds
Add Bonds Manually
Menubar: Edit > Bond > Add Atom By Atom

Repeats adding bonds until End is selected.
Command Line: ADD BOND origin_atom target_atom
• origin_atom—Atom at beginning of bond.
• target_atom—Atom at end of bond.
The bond type of the new bond is set by the atom types at its endpoints. If there
is ambiguity regarding the bond type, a prompt asks for the resolution. Atomic
positions are not altered by adding a bond.
Add Bonds Automatically
Single bonds may also be added using the Quick Bonds functionality. SYBYL
adds a single bond between two atoms if the distance between them is within an
acceptable range. This is particularly useful for PDB files containing discon-
nected HETATM records.
Menubar: Edit > Bond > Add Quick Bonds

Command Line: QUICKBOND mol_area atom_expr
• mol_area—Work area containing the molecule.
• atom_expr—Atoms between which connectivities must
be identified.

SYBYL adds a bond between two atoms, A and B, if the distance between
them, DISTAB, is within acceptable range:
Ideal_Bond(1-Tol_Neg) < DistAB < Ideal_Bond (1+Tol_Pos) [EQ 1]

where:
• Ideal_Bond—Standard bond length between atom types A and B in
the bond length table.
• Tol_Neg—Tolerance used to determine low end of the distance
range. This Tailor variable has a default of 0.30.
• Tol_Pos—Tolerance used to determine high end of the distance
range. This Tailor variable has a default of 0.10.
The asymmetry of the acceptance window (Tol_Neg > Tol_Pos) allows for
alkynes (Ideal_Bond = ~1.15 Å) and certain short aromatic C-C bonds to be
recognized as bonds without making chemical oddities from non-covalent
intramolecular hydrogen bonding patterns.
By adding only single bonds, molecular connectivity can be determined with a

high degree of accuracy and minimum user intervention. Check all atom and
bond types within the specified atom expression before proceeding with calcula-
tions, where this information is relevant.
• TAILOR SET CONNECT to alter the characteristics of the connectivity
determination.
Delete Bonds
Menubar and toolbar do not require pre-selection, but will act on pre-selected
atoms by deleting the bond(s) between them.
Menubar: Edit > Delete > Bonds

Toolbar:
> Bonds
Command Line: REMOVE BOND bond_expr
Features (rotatable bonds) associated with the deleted bond are removed as well.
Bonds are renumbered to reflect the removal of objects from the molecular
description. If one of the two last atoms in a substructure is a biopolymer atom
(as defined in the macromol dictionary), SYBYL retains the root atom in the
substructure and the other atom in the substructure zero.

Delete Bond Attributes
Attributes can be removed from one or more bonds without deleting the bonds
themselves.
Command Line: REMOVE ALL_BOND_ATTRS expression
Modify a Bond
Modify Type via the Edit > Bond > Modify Type
Menubar:
Modify Type via MODIFY BOND AUTO_TYPE|TYPE bond_expr
Command Line: {type}
• AUTO_TYPE—Force the automatic determination
of bond type according to types of atoms at each
end of the bond. Only prompts for bonds whose
types are ambiguous.
• TYPE—Prompt for type for each specified bond.
No adjustment of parameters other than type is
attempted for selected bonds.
Modify Length via Edit > Bond > Modify Distance
the Menubar:
Modify Length via MODIFY DISTANCE atom1 atom2 value
Command Line:
Modify Angle via the Edit > Bond > Modify Angle
Menubar:
Modify Angle via MODIFY ANGLE atom1 atom2 atom3 angle
Command Line:
Modify Torsion via Edit > Bond > Modify Torsion
the Menubar:
Modify Torsion via MODIFY TORSION atom1 atom2 atom3 atom4
Command Line: angle
When changing the length, angle, or torsion, SYBYL alters the coordinates of
last specified item and all atoms attached to it. The atoms must be connected to
form a bond, angle, or torsion, respectively. If the bond, angle, or torsion is in a
ring, an error is reported and no alteration is made.

8.5.3 Chemical Group

You can add a functional group to the molecular structure and have their
geometry determined from the parameter tables. The atoms in the group and
their relative positions are read from the Group Library.

Command Line: ADD GROUP group_name ATTACH | REPLACE atom
• group_name—Name of group to add to structure. (Type
“?” at prompt to list available groups.)
• ATTACH—Add new group to specified atom with appro-
priate geometry.
• REPLACE—Remove specified atom and add new group
in its place, with ideal geometry (useful when
hydrogens are present).
• atom—Atom for attachment or to replace.
The permission on the Group Library should normally be “read only” to prevent
accidental modification. However, the Group Library is user expandable, and
before adding a group to this library, you must change the permission on the file
$TA_DATA/GROUP to allow writing:
chmod +w $TA_DATA/GROUP
Set the permission back to read only after the group has been added:
chmod -w $TA_DATA/GROUP
• See Group Library Structure and Contents on page 232.

8.5.4 Delete or Modify Substructures
Delete Substructures
Menubar: Select the substructure(s) to be deleted, then

Edit > Delete > Selected or Selected Atoms
Icon:
Click on the Edit toolbar to delete the current
selection.
Command Line: REMOVE SUBSTRUCTURE expression
• expression—Substructure expression indicating
substructure(s) to delete.
Modify Substructures
Substructure modification is not accessible from the menubar.
Modify a Substructure’s Name:
MODIFY SUBSTRUCTURE NAME substructure_expr {mode name}

• substructure_expr—Substructures to modify.
• mode:
APPEND_AUTO—Single string is supplied and concatenated with selected
substructure’s current name.
QUERY—Name for each selected substructure is entered. Each selected
substructure is highlighted as you are prompted for its name.
SEQUENTIAL_AUTO—Element type name is concatenated with
substructure ID number.
• name—Name or fragment thereof to associate with the substructure in
all but SEQUENTIAL_AUTO mode. First character must be alphabetic and
may contain alphabetic, numeric, and the apostrophe.
To rename substructures (residues) in a biopolymer, use the BIOPOLYMER

RENUMBER command.
Modify a Substructure’s Root Atom:
MODIFY SUBSTRUCTURE ROOT substructure_expr {atom_sel}

• atom_sel—Atom to be the root of each of the selected substructures.

Substructures are composed of connected atoms forming a “graph” structure.

The graph is traversed from the “root” to all other atoms in the substructure. All
bonds within the substructures are ordered such that when traversed from origin
to terminus, they are directed away from the root. The original root is selected
arbitrarily by the program. This command alters the root of the substructure and
re-orders the graph.
Modify a Substructure’s Type:
MODIFY SUBSTRUCTURE TYPE substructure_expr {type}

• type—DOMAIN, GROUP, PERMANENT, RESIDUE, TEMPORARY.
All types that are not temporary are permanent. Only RESIDUE has any special
meaning. It is used extensively in the manipulation of biopolymers where it is
synonymous with monomer. Generally you should not alter the substructure
types; they are managed by the system.
Create/Modify a Substructure’s Comment:
MODIFY SUBSTRUCTURE COMMENT substructure_expr {comment}

• comment—Descriptive string. It may contain any characters and be of
arbitrary length. Use double quotes when entering spaces or special
characters via command line.
8.5.5 Chirality
Determine Chirality
Menubar: Edit > Chirality > Find

Command Line: • CHIRAL PRO_RS atom_expr—Determine PRO-R or
PRO-S chirality of the specified atoms.
• CHIRAL RS atom_expr—Determine R or S chirality
of the specified atoms.
• CHIRAL ZE bond_expr—Determine Z or E
isomerism about the specified double bonds.
• CHIRAL MARK_RS atom_expr—Determine R or S
chirality of the specified atoms and set the atom
chirality attribute.
• CHIRAL MARK_ZE bond_expr—Determine Z or E
isomerism about the specified double bonds and set the
bond stereo attribute.

Both the chirality of an atom and the cis-trans isomerism about a double bond
can be determined by using a set of rules developed by Cahn, Ingold and Prelog
and adopted by IUPAC (See J. Org. Chem., 35, 9, 2849, (1970)). These rules
govern the sequencing of substituents about the chiral atom or double bond.
Once the substituents are assigned a priority, simple geometric algorithms
determine which type of isomerism is present. These same rules are used to
determine the prochirality of an atom.
The system determines the RS isomerism of an atom by positioning a three-

dimensional representation of the atom so that the lowest group in the sequence
is oriented away from the viewer. If the remaining substituents are arranged in a
clockwise manner by priority, the center is designated R, otherwise it is S.
ZE isomerism about a double bond is a more general designation than cis-trans;

it is determined by examining the bond’s substituents and sequencing them in
the manner prescribed by IUPAC (atomic number is the first criterion) which
encompasses the Cahn/Ingold/Prelog sequencing rules. The special relationship
between the higher priority substituent on each end of the double bond is
examined relative to a reference plane, which includes the two double bonded
atoms, and drawn perpendicular to the plane of the four substituents. If the two
higher priority substituents lie on the same side of this reference plane, the
isomerism is denoted as Z; if they lie on opposite side, it is E.
Atom chirality attributes are used by the expression generator %sln() when
converting a SYBYL molecule to an SLN string. The chirality will then be
expressed as [S=N] or [S=I] (see the SLN Manual for details). The bond stereo
attributes are also used by the expression generator %sln().
Any unfilled valences are assumed to be occupied by hydrogens.
The built-in set {CHIRAL} determines only RS isomerism.
• TAILOR SET CHIRAL to alter the method for calculating chirality.
Invert Chirality
Menubar: Edit > Chirality > Invert

Command Line: INVERT atom_expr
If all atoms in the molecule are to be inverted, the entire molecule is inverted by
reflecting the X-coordinate through the YZ plane. Otherwise, each individual
tetrahedral atom is inverted by exchanging two substituents. Note that non-
chiral centers may also be inverted.

Atoms at ring fusions cannot be inverted individually, but only as part of the
inversion of the whole molecule.
No chirality determination is done before or after the inversion. A message is

issued only if a selected center cannot be inverted due to a ring fusion. A count
of the number of tetrahedral centers successfully inverted is given.
If a molecule includes atom chirality attributes, these attributes are inverted as

well as the coordinates of the chosen atoms. Atom chirality attributes are set
either by the CHIRAL_MARK_RS command or by using the expression generator
%sln_to_mol() to convert an SLN string to a SYBYL molecule.
Reflect Atoms Through a Plane
Menubar: Edit > Chirality > Reflect through Plane

Command Line: REFLECT atom_expr plane_name
• atom_expr—Atoms to reflect through the plane.
• plane_name—Name of plane through which reflection
is done.
The plane must be defined on the molecule. Any arbitrary atoms may be
reflected through the plane. Examine the resulting bonding geometry carefully,
since the program pays no attention to the geometrical arrangement during this
operation.
• DEFINE PLANE to calculate the equation of the plane.
Delete Stereo Atom Attribute from a Molecule Description
Delete the stereo atom attributes.

Command Line: REMOVE STEREO_ATOM_ATTR expression
Delete Stereo Bond Attribute from a Molecule Description
Delete the stereo bond attributes.

Command Line: REMOVE STEREO_BOND_ATTR expression

8.5.6 Center of Rotation, Name, Type, etc. of a Molecule
Change Center of MODIFY MOLECULE CENTER_OF_ROTATION

Rotation via Com- mol_area atom_sel
mand Line: • mol_area—Molecule area containing molecule.
• atom_sel—Atom(s) to use as center of rotation.
Or
CENTER atom_expr
Computes the average X, Y and Z for the specified group
of atoms and translates the molecule so that this position
becomes the origin of the molecule coordinate system.
Reset will restore the original coordinates. For more
information see CENTER (in the Graphics Manual).
To save the new coordinates, use FREEZE in the Graph-
ics Manual).
To simply view the molecule in the center of the screen
without affecting its coordinates use CENTERVIEW (in
the Graphics Manual).
Create/Modify MODIFY MOLECULE COMMENT area {comment}
Comment via • area—Area(s) containing molecule(s) to modify.
Command Line: • comment—Descriptive string, may contain any
characters and be of arbitrary length. Use double
quotes when entering spaces or special characters
via command line.
Create/Modify Edit > Molecule > Name
Name via • At least one atom must have been pre-selected.
Menubar: • If atoms were selected in multiple molecule areas
you will be prompted to specify which molecule
area contains the molecule to be named.
Create/Modify MODIFY MOLECULE NAME area {name}
Name via Com- • area—Area(s) containing molecule(s) to modify.
mand Line: • name—Name to identify molecule and key for its
storage and access in database. If molecules are
saved into a SYBYL Mol2 database, filenames are
generated from molecule names. For database use,
avoid names containing: colon (:), question (?),
backslash (\), and space ( ). If the file and molecule
name are to be manipulated in SPL, avoid:
circumflex (^) and pipe (|).
Names are required before adding a molecule to a data-
base (see Add Molecule(s) to a Database on page 174).

Change Root via MODIFY MOLECULE ROOT mol_area

Command Line: {substructure_sel comment}
• mol_area—Area(s) containing molecule(s) to
modify.
• substructure_sel—Substructure to be the root of the
molecule tree.
• comment—Comment to store with new root.
Molecules may have any number of independent con-
nected fragments, each one composed of at least a sin-
gle substructure. Each fragment has one of its
substructures recorded in the molecule header, i.e., the
“root” of the fragment “tree”.
Change Type via MODIFY MOLECULE TYPE mol_area {type}
Command Line • mol_area—Area(s) containing molecule(s) to
modify.
• type—NUCLEIC_ACID_MOLECULE,
SACCHARIDE_MOLECULE, PROTEIN,
SMALL_MOLECULE, MACRO_MOLECULE.
8.5.7 Combine (Fuse) Two Molecules

Command Line: FUSE {atom_pairs}
The two structures do not have to be cyclic. At least two atoms must be selected
in each molecule; more atoms help direct fusion of non planar bonds. Terminate
the input list with the end-loop character (|).
SYBYL places the fused structure in the molecule area of the first atom of each
pair. Coordinates of atoms used for the fusion are taken from the first molecule.
The bonds directly connecting fusion atoms in each molecule are discarded. An
attempt is made to retain all other bonds in both molecules. If the atomic
valence of the fusion atom is exceeded, any Hs attached to fusing atoms are
discarded and the fusion rechecked. If the operation still fails, an error is
reported and the command terminated. You must then discard enough atoms to
make fusion legal. If the operation succeeds, Hs are replaced to fill valences of
atoms from which they were removed.
If you specify fusion of two molecules across an aromatic or double bond by

selecting only two atoms, alignment of resulting fragments is unambiguous. If,
however, fusion across a single bond involving tetrahedral atoms is specified by
two atoms, ambiguity arises. The program attempts to select the alternative
which results in the best fusion geometry. If you prefer another alternative
fusion geometry, select three or more atoms to unambiguously establish the
geometry.

Spiro fusions cannot be specified by selecting a single atom pair. They can be
specified by adding Hs and indicating the fusion of an internal bond in one
molecule with the bond involving the H atom.
• Ring Fusion Tutorial on page 103.
• TAILOR SET FUSE to select default parameter set to alter character-
istics of the fusion.
8.5.8 Combine (Join) Two Molecules

Command Line: JOIN target_atom new_group_atom
• target_atom—Atom to replace with group being added.
• new_group_atom—Atom in joining group being
discarded when group is fused to molecule.
This functionality cannot be used to form a ring closure bond.
The length of the new bond is determined by the type of the atoms being joined
and is taken from a table of standard bond lengths. The two atoms specified are
eliminated by the join operation.
Groups being joined may be in same molecule area or in different areas. In the
latter case, atoms to be joined are copied into the target atom’s molecule area
and then the bond formed.
• Add Bonds Manually on page 125 to connect two atoms.
• Merge Molecule Areas on page 56.
• TAILOR SET JOIN to customize the parameters for joining.
8.5.9 Adjust Bond Lengths and Angles to Match Standards

The Shaked algorithm iteratively loops through the selected atoms, adjusting
bond lengths and bond angles, to more closely match standard values stored in
the bond length and the Tripos force field bond angle tables.
Corrections are applied to coordinates to satisfy distance constraints:
L ij ≤ D ij ≤ U ij [EQ 2]

Where Lij is the lower bound for the distance (Dij) between atoms i and j, and
Uij is the upper bound. A delta of 0.05 is added to or subtracted from the value
obtained from the parameter tables to derive the upper and lower bounds,
respectively.
This operation is performed until either the maximum number of iterations

(100) is reached or convergence has occurred, that is, all constraints are met.
The algorithm fails when distance constraints are inconsistent or the input
structure is very different from the structure that obeys all distant constraints.
This algorithm is described by I. Haneef, Simon J. Talbot, and Peter G.

Stockley in J. Mol. Graphics, 7, 186-195 (1989).
Menubar: Edit > Clean-Up Molecule > Shake Bonds and

Angles
Acts on selected atoms in a single molecule area.
Command Line: SHAKED atom_expr
8.5.10 Scan Torsions to Reduce van der Waals Contacts
Menubar: Edit > Clean-up Molecule > Scan Torsions

Acts on selected bonds in a single molecule area.
Command Line: SCAN bond_expr
The specified torsion angles are scanned, through a full 360°, for positions
which relieve bad steric interactions. Only one bond at a time is altered. After a
position is found, that bond is removed from the set being considered. Scanning
continues until all interactions dependent upon these bonds are relieved or until
no progress is made from one iteration to the next. Interrupt the process by
typing <control> C.
• TAILOR SET SCAN to alter characteristics of the scan.
• The following BIOPOLYMER subcommands: ADD_SIDECHAIN, CHANGE,
INSERT, JOIN, SET CONFORMATION.
8.5.11 Create a Molecule by Averaging Existing Molecules

AVERAGE_MOL mol_expr mol_area
mol_expr Expression indicating location of existing molecules.

Empty molecule areas are ignored.

mol_area Area in which to place new molecule. Default is lowest

numbered empty molecule area.
Assuming the starting set of molecules are different conformations of the same
structure, this command creates another conformation (of the same molecule)
where:
• Coordinates of every atom are the average of the X, Y, Z coordinates of
corresponding atoms in selected molecules.
• All other aspects of the molecule (bonds, substructures, features, etc.)
are taken (arbitrarily) from one of the selected molecules.
If the selected molecules do not all contain the same number of atoms, an error
message is displayed and no molecule is created. Make sure all other aspects of
the molecules are consistent (bonds, substructures, etc.).

Define and Modify Geometric Features
8.6 Define and Modify Geometric Features

• Center of Mass on page 138
• Centroid on page 139
• Extension Point on page 140
• Line on page 141
• Normal to a Plane on page 142
• Plane on page 143
• Renumber Atoms on page 144
• UNITY Query Features on page 145
Note:
Whole or partial re-orientation (via Fit Atoms, Freeze Molecule, ORIENT,
geometrical modification or manipulation of rotatable bonds) after defining
centers of mass, centroids, extension points, normals, or planes renders the
feature invalid. Use the EVALUATE command to update the feature’s position.
• VISUALIZE, in the Graphics Manual, to display some of the defined
features.
• List Information About SYBYL Objects on page 155.
8.6.1 Center of Mass

A centroid is a dummy atom at the center of a group of atoms. The center of
mass is a centroid with coordinates weighted by the atomic masses. When
defined, the dummy atom is added to the coordinate list and a feature in the
molecular description. The dummy atom is connected through a dummy bond to
the atom used in the calculation closest to its position. Dummy atoms have the
type Du and are colored magenta.
Note: Atomic weights now (SYBYL 7.1) correlate with the latest accepted
figures from IUPAC and NIST. The average difference is 0.01% of the values in
SYBYL 7.0. For unstable atoms, the values for the most stable isotope are used.
• IUPAC: Pure Appl. Chem., Vol.75, No.8, pp 1107-1122, 2003.
• National Institutes of Standards and Technology (NIST)
For more information, see $TA_ROOT/sybylbase/tables/metals/ATOM_DEF

Define DEFINE CENTER_OF_MASS atoms center_name comment

Re-Evaluate: EVALUATE CENTER_OF_MASS mol_area name
• mol_area—Area(s) containing center(s) of mass to
evaluate.
• name—Name of center(s) of mass to evaluate. Enter a
question mark (?) to list names. Expression may include
the wildcard character (*) (e.g., to remove both c1 and c2,
enter c*, but the expression c1,c2 is not valid).
The new coordinates are computed and stored in the molecular
definition. In addition, dummy atoms representing the position
of the features are adjusted to reflect the new values.
Remove REMOVE CENTER_OF_MASS mol_area name
• mol_area—Area(s) containing center(s) of mass to delete.
• name—Name of center(s) of mass to delete.
8.6.2 Centroid
A centroid is a dummy atom at the center of a group of atoms. When defined, it
is added to the coordinate list and a feature in the molecular description. The
dummy atom is connected through a dummy bond to the atom used in the calcu-
lation closest to its position. Dummy atoms have the type Du and are colored
magenta. (See TAILOR SET CENTROID to alter the characteristics of the
centroid.)
Define via the Edit > Centroid > Define

Menubar:
Define via Com- DEFINE CENTROID atom_expr centroid_name com-
mand Line: ment
Re-Evaluate: EVALUATE CENTROID mol_area name
• mol_area—Area(s) containing centroid(s) to evaluate.
• name—Name of centroid(s) to evaluate. Enter a
question mark (?) to list names. Expression may
include the wildcard character (*) (e.g., to remove both
c1 and c2, enter c*, but the expression c1,c2 is not
valid).
The new coordinates are computed and stored in the
molecular definition. In addition, dummy atoms represent-
ing the position of the features are adjusted to reflect the
new values.
Remove via the Edit > Centroid > Delete
Menubar:

Remove via REMOVE CENTROID mol_area name

Command Line: • mol_area—Area(s) containing centroid(s) to delete.
• name—Name of centroid(s) to delete.
Any features (plane, normal, constraint) attached to that
centroid are removed as well.
8.6.3 Extension Point

An extension point is a dummy atom connected to the molecule that can be used
as a place holder. The extension point can represent a ligand atom or a hydrogen
bond partner. It is added as a dummy atom in the coordinate list and a feature in
the molecular description. It is connected through a dummy bond to atom1.
Define DEFINE EXTENSION_POINT atom1 atom2 atom3 dist

ang tors name comment
• atom1, atom2, atom3—IDs of atoms defining extension
point. If any are lone pairs, use the command MODIFY
ATOM LONE_PAIR first.
• dist—Distance of extension point to atom1.
• ang—Angle for extension point, atom1, and atom2.
• tors—Torsion angle for extension point, atom1, atom2, and
atom3.
• name—Name for extension point.
• comment—Arbitrary string associated with the extension
point.
Re-Evaluate: EVALUATE EXTENSION_POINT mol_area name
• mol_area—Area(s) containing point(s) to evaluate.
• name—Name of point(s) to evaluate. Enter a question mark
(?) to list names. Expression may include the wildcard
character (*) (e.g., to remove both c1 and c2, enter c*, but
the expression c1,c2 is not valid).
Remove REMOVE EXTENSION_POINT mol_area name
• mol_area—Area(s) containing point(s) to delete.
• name—Name of point(s) to delete.

8.6.4 Line
A line adds a dummy atom at a specified distance along the path between two
atoms.
Define DEFINE LINE origin_atom positive_atom dist name

comment
• origin_atom—Atom defining origin of line.
• positive_atom—Atom defining direction of line from
origin_atom.
• dist—Distance (Å) from origin_atom to dummy atom.
Positive value indicates “towards” positive_atom, a
negative value corresponds to “away from.”
• name—Name for line.
• comment—Arbitrary string associated with line and
dummy atom.
Re-Evaluate: EVALUATE LINE mol_area name
• mol_area—Area(s) containing line(s) to evaluate.
• name—Name of line(s) to evaluate. Enter a question mark
(?) to list names. Expression may include the wildcard
character (*) (e.g., to remove both c1 and c2, enter c*, but
the expression c1,c2 is not valid).
Remove REMOVE LINE mol_area name
• mol_area—Area(s) containing line(s) to delete.
• name—Name of line(s) to delete.

8.6.5 Normal to a Plane

A normal is a line normal to an existing plane through an atom.The normal is
represented by two dummy atoms on either side of a specified atom. Two
dummy bonds connect them to the midpoint. The bonds are perpendicular to the
specified plane. Distance from the midpoint to the dummy atoms is a variable
set at 1 Å by default. The normal is stored as two dummy atoms, two dummy
bonds and a feature in the molecular description. Dummy atoms have the type
Du and are colored magenta.
Define via the Edit > Normal > Define

Menubar:
Define via Com- DEFINE NORMAL atom_sel plane_name
mand Line: normal_name comment
The two dummy atoms are named “normal_name” fol-
lowed by 1 or 2.
Re-Evaluate: EVALUATE NORMAL mol_area name
• mol_area—Area(s) containing normal(s) to evaluate.
• name—Name of normal(s) to evaluate. Enter a
question mark (?) to list names. Expression may
include the wildcard character (*) (e.g., to remove both
c1 and c2, enter c*, but the expression c1,c2 is not
valid).
Plane coordinates and plane normal lines are not updated
after whole or partial re-orientation of the molecule (via
Fit Atoms, Freeze Molecule, ORIENT, geometrical modifi-
cation or manipulation of rotatable bonds). Use the EVAL-
UATE PLANE command first then re-evaluate the normal
line(s).
Remove via the Edit > Normal > Delete
Menubar:
Remove via REMOVE NORMAL mol_area name
Command Line: • mol_area—Area(s) containing normal(s) to delete.
• name—Name of normal(s) to delete.
Any features (e.g., constraints) attached to that normal are
removed as well. If an atom, real or artificial, and involved
in a normal definition, is removed, the normal is removed
automatically.
• See Plane on page 143 for information about how to define the required
plane.
• See TAILOR SET NORMAL to alter the characteristics of the normal.

8.6.6 Plane
A plane is represented by four dummy atoms connected by four dummy bonds
delineating a parallelogram. (See TAILOR SET PLANE to alter the character-
istics of the plane.) The plane is stored as four dummy atoms, four dummy
bonds and a feature in the molecular description.Dummy atoms have the type
Du and are colored magenta.
Define via the Edit > Plane > Define

Menubar:
Define via Com- DEFINE PLANE atom_expr plane_name comment
mand Line: • atom_expr—The atoms to use in calculating the plane
equation: from a minimum of 3 non-linear atoms up to
all the atoms in the molecule.
• plane_name—Name to give to the new plane
• comment—An arbitrary string associated with the
plane
The four dummy atoms are named “plane_name” followed
by 1, 2, 3, or 4.
The equation of the least squares plane is printed in the
console along with the RMS distance of the defining
atoms to the plane.
Re-Evaluate: EVALUATE PLANE mol_area name
• mol_area—Area(s) containing plane(s) to evaluate.
• name—Name of plane(s) to evaluate. Enter a question
mark (?) to list names. Expression may include the
wildcard character (*) (e.g., to remove both c1 and c2,
enter c*, but the expression c1,c2 is not valid).
Use this feature to update the plane equation and dummy
atom coordinates after whole or partial re-orientation of
the molecule (via Fit Atoms, Freeze Molecule, ORIENT,
geometrical modification or manipulation of rotatable
bonds). Lines normal to a plane, if present, must be re-
evaluated via the EVALUATE NORMAL command.
Remove via the Edit > Plane > Delete
Menubar:
Remove via REMOVE PLANE mol_area name
Command Line: • mol_area—Area(s) containing plane(s) to delete.
• name—Name of plane(s) to delete.
Any features (e.g., constraints) attached to that plane are
deleted along with the plane. If an atom, real or artificial,
and involved in a plane definition, is removed, the plane is
removed automatically.

• Normal to a Plane on page 142 for using a plane to define a normal.
• Reflect Atoms Through a Plane on page 132
8.6.7 Renumber Atoms

Renumbering atoms imposes an arbitrary order on atoms in a molecule for the
purposes of Z-matrix formation. It is done prior to submitting the molecule to
quantum mechanical calculations.

Command RENUMBER origin_area target_area {atom_sel}
Line: • origin_area—Area containing molecule to renumber.
• target_area—Area to receive renumbered molecule.
• atom_sel—Atoms to renumber, in the new numerical order.
Renumbering atoms causes all defined features to be deleted from the molecule
because there is no automatic translation from the internal representation of the
feature definition to atom numbers. All other information about the molecule is
suitably transformed and restored after renumbering.
You are prompted for the ID number of the atom you want in each position. (To
display current atom numbers, use LABEL ID * before renumbering.) Positions
are given in sequence from 1 to the number of atoms in the molecule. Specifi-
cation can be terminated at any time. Atoms not specified to be renumbered
retain their relative order and are added to the molecule list immediately behind
atoms which were renumbered.

8.6.8 UNITY Query Features

A UNITY geometrical feature or constraint for a structure is used within a
UNITY database query. UNITY features are displayed as background objects
and can be saved as part of the molecular definition. The TAILOR SET UNITY
command can be used to select the color for highlighting constraints, features,
and receptor sites.
For details on defining specific features and constraints, see the “UNITY
Queries” chapter, in the UNITY Manual.
Define via the UNITY > Edit Query > Add Features
Menubar:
Define via DEFINE UNITY_FEATURE option
Command Line:
• 4_POINT_ANGLE_CONSTR • LINE
AINT • LP_ANGLE_CONSTRAINT
• ACCEPTOR_ATOM • NEGATIVE_CENTER
• ACCEPTOR_SITE • NORMAL_POINT
• ANGLE_CONSTRAINT • PARTIAL_MATCH_CONSTR
• AROMATIC AINT
• BOND_PATH • PLANE
• CENTROID • POSITIVE_N
• RECEPTOR_SITE
• CONTAINING_VOLUME_CO • SPATIAL_CAP
NSTRAINT • SPATIAL_LINE
• DISTANCE_CONSTRAINT • SPATIAL_PLANE
• DONOR_ATOM • SPATIAL_POINT
• DONOR_SITE
• EXCLUDED_VOLUME_CONS • STERIC_FEATURE
TRAINT • SURFACE_VOLUME
• EXTENSION_POINT • TETRAHEDRAL
• FRAGMENT • TORUS
• HYDROPHOBIC
Delete Non- UNITY > Edit Query > Delete > Atoms not in the
Query Atoms Query
via the The list of atoms to remove is displayed in the atom
Menubar: expression dialog and highlighted on the molecule.
Changes to the atom expression may be made before
pressing OK to remove the atoms.

Delete Non- REMOVE NON_QUERY_ATOMS mol_area

Query Atoms • mol_area—Area containing the UNITY query.
via Command A list of atoms to remove is displayed in the atom expres-
Line: sion dialog and highlighted in the molecule. Changes to
the atom expression may be made before pressing OK to
remove the atoms. If the molecule area does not contain
any UNITY features or constraints, no action is taken.
Modify via the UNITY > Edit Query > Manage Features
Menubar:
Modify via MODIFY UNITY_FEATURE mol_area feature/con-
Command Line: straint [{attribute value}] [COLOR]
• mol_area—Molecule area containing feature or
constraint.
• feature/constraint—Feature or constraint to modify.
• attribute—Name of an attribute. Modifiable attributes
are type-specific, and depend on feature or constraint
selected.
• value—Value for the attribute.
• COLOR—Optional for UNITY features only.
Remove via the UNITY > Edit Query > Delete > Features
Menubar: UNITY > Edit Query > Manage Features
Remove via REMOVE UNITY_FEATURE mol_area name
Command Line: • mol_area—Area containing feature or constraint.
• name—Name of UNITY feature or constraint to
delete. Type ALL instead of a single name to delete all
features and constraints.
Any constraints based on that feature are removed as well.
If an atom, real or artificial, and involved in a feature or
constraint definition, is removed, the feature or constraint
is removed automatically.

Chapter 9.
Geometric Measurements
• Intra-/Intermolecular Measurements on page 148

• List Coordinates, Distances, or Angles on page 149
• Measure the Intramolecular Angle Between Planes on page 150
• Measurements Specific to UNITY Features on page 151
• BIOPOLYMER MEASURE to measure omega and zeta angles.
• TAILOR SET GENERAL ANGLE_RANGE to specify how an angle range
should be displayed.

Chapter 9. Geometric Measurements
Intra-/Intermolecular Measurements
9.1 Intra-/Intermolecular Measurements

Angles
Menubar: Compute > Measure > Angle

Command Line: MEASURE ANGLE {atom1 atom2 atom3}
Loops until you type the end-loop character (|).
UIMS2 Variable: MEASURE_ANGLE
Distance
Menubar: Compute > Measure > Distance

Command Line: MEASURE DISTANCE {atom1 atom2}
UIMS2 Variable: MEASURE_DISTANCE
Height of Atoms Above Plane
Menubar: Compute > Measure > Height Above Plane

Command Line: MEASURE HEIGHT atom_expr plane_name
• atom_expr—Atoms whose height is to be measured.
• plane_name—Name of plane, in default work area, to
use. Use LIST PLANE to find names of defined planes.
Note: Plane coordinates and plane normal lines are not
updated when you use FREEZE. Use EVALUATE PLANE
mol_area name, then EVALUATE NORMAL mol_area
name to update the plane and normal line.
UIMS2 Variable: MEASURE_HEIGHT
Torsion Angles
Menubar: Compute > Measure > Torsion

Command Line: MEASURE TORSION {atom1 atom2 atom3 atom4}
UIMS2 Variable: MEASURE_TORSION
• List Coordinates, Distances, or Angles on page 149.

List Coordinates, Distances, or Angles
9.2 List Coordinates, Distances, or Angles

Menubar: Compute > Measure > Topography
List Bond Angles TOPOGRAPHY ANGLES atom_expr
via Command • atom_expr—Expression indicating angle(s). All
Line: angles having the center atom in this atom
expression are listed
List Bond Lengths TOPOGRAPHY BOND_LENGTH atom_expr
via Command • atom_expr—Expression indicating bond(s). All
Line: bonds having either their origin or their target in
this expression are listed.
List Coordinates TOPOGRAPHY COORDINATES atom_expr
via Command • atom_expr—Expression indicating atoms whose
Line: coordinates are to be listed.
Coordinates listed by this command are affected by
rotations and translations applied to molecule on the
terminal. To list coordinates in memory, use the LIST
ATOMS command. Alternatively, cancel rotation/transla-
tion matrix using the reset feature on your terminal, or
FREEZE coordinates before issuing the TOPOGRAPHY
command.
List Non-bonded TOPOGRAPHY NON_BONDED_LENGTH atom_expr1
Distance via Com- atom_expr2
mand Line: Distances between every atom in atom_expr1 and every
atom in atom_expr2 are listed.
List Torsion TOPOGRAPHY TORSION_ANGLE bond_expr
Angles via Com- • bond_expr—Expression indicating torsion(s). All
mand Line: torsion angles having the center bond in this bond
expression are listed.
• Record the Output from a Single Command on page 194.
• Intra-/Intermolecular Measurements on page 148.
• BIOPOLYMER MEASURE to conveniently measure omega and zeta angles.
• BIOPOLYMER CHECK_GEOMETRY to report deviations from standard
geometry.

Measure the Intramolecular Angle Between Planes
9.3 Measure the Intramolecular Angle Between

Planes
Menubar: Compute > Measure > Plane Angle
Command Line: MEASURE PLANE_ANGLE mol_area plane_name1
plane_name2
Use LIST PLANE to find names of defined planes.
Note: Plane coordinates and plane normal lines are not
updated when you use FREEZE. Use EVALUATE PLANE
mol_area name, then EVALUATE NORMAL mol_area
name to update the plane and normal line.
UIMS2 Variable: MEASURE_PLANE_ANGLE

Measurements Specific to UNITY Features
9.4 Measurements Specific to UNITY Features

MEASURE UNITY_MEASUREMENTS mol_area option
Option:
ANGLE atom1 atom2 atom3 Measure angle of atoms.

DISTANCE atom1, atom2 Measure distance between atoms.
HEIGHT atom_expr plane_name Measure height of atom above plane.
PLANE_ANGLE plane_name1 Measure angle between planes in
plane_name2 same work area.
TORSION atom1 atom2 atom3 Measure torsion angle of atoms.
atom4

Chapter 10.
Get Information on SYBYL Objects
• Information on Selected Objects on page 154

• Right-Click for Information on page 154
• Atoms, Bonds, or Substructures on page 154
• List Information About SYBYL Objects on page 155
• Print Information About SYBYL Objects on page 156

Chapter 10. Get Information on SYBYL Objects
Information on Selected Objects
10.1 Information on Selected Objects

10.1.1 Right-Click for Information
Atom right-click > Molecule Properties
A dialog displays the name of the molecule and the computed values of
several physical and chemical properties.
Atom right-click > Atom Properties

A dialog displays the atom’s name and that of the molecule it belongs to as
well as several computed properties.
10.1.2 Atoms, Bonds, or Substructures

Report information about the selected object in the console.
Menubar: Options > Info

• Atom then click the atom(s) of interest
• Bond then click two bonded atoms
• Substructure then click any atom in the substructure
(residue) of interest.
Press End to terminate the information loop.
Command INFORMATION object_type object_sel
Line: • object_type—ATOMS, BONDS, SUBSTRUCTURES.
• object_sel—ID for individual object. Prompting continues
until you enter the end-loop character (|).

List Information About SYBYL Objects
10.2 List Information About SYBYL Objects

Menubar: Options > List
Command LIST object_type object_expr [mode]
Line: • object_type—AGGREGATES, ATOMS, BACKGROUNDS,
BONDS, BUILT_IN_SETS, CENTER_OF_MASS, CENTROID,
CONSTRAINT, EXTENSION_POINT, GLOBAL_SETS, LINE,
LOCAL_SETS, MOLECULES, NORMAL, PLANE, SEQUENCE,
SUBSTRUCTURES, TABLE, TAILOR, UNITY_FEATURE,
VIOLATIONS.
• object_expr—Particular set of objects of object_type to
list.
• mode—BRIEF (one line summary for each object or FULL
(all available information for each object) for most
objects. ALL, TYPE, or NAME for UNITY features. (In
picking mode, NAME allows picking on the screen of a
particular feature.)
In the atom, bond, and substructure list, an asterisk (*) in the column following
the ID indicates that the object belongs to an internal ring (i.e., a ring totally
contained within a substructure), whereas an “at” sign (@) indicates an external
ring (i.e., a ring which spans substructure boundaries). Substructures cannot
participate in internal rings but they can be members of external rings.
For sets, an asterisk (*) in the column after the ID indicates that the set is
defined and managed by the system.
• Record the Output from a Single Command on page 194 to copy the
listing into a file.
• Define and Modify Geometric Features on page 138.
• TAILOR SET GENERAL ATOM_IDENTIFIER to alter the characteristics
of atom listings.

Print Information About SYBYL Objects
10.3 Print Information About SYBYL Objects

PRINT object_type object_expr [mode]
object_type Type of object to include in the output:

AGGREGATES, ATOMS, BACKGROUNDS, BONDS,
BUILT_IN_SETS, CENTER_OF_MASS, CENTROID, CON-
STRAINT, EXTENSION_POINT, GLOBAL_SETS, LINE,
LOCAL_SETS, MOLECULES, NORMAL, PLANE, SEQUENCE, SUB-
STRUCTURES, TABLE, TAILOR, VIOLATIONS.
object_expr Objects to include in the output.
mode Listing mode to use (BRIEF or FULL). This argument does not
apply to all objects.
Use the full generality of the object expression syntax to determine which
objects to include. The PRINT command writes out the file SYBYLPRINT.LIS and
submits it to lpr for printing.
In the atom, bond, and substructure list, an asterisk (*) in the column following
the ID indicates that the object belongs to an internal ring (that is, a ring totally
contained within a substructure), whereas an “at” sign (@) indicates an external
ring (a ring which spans substructure boundaries). Substructures cannot partic-
ipate in internal rings but they can be members of external rings.
For sets, an asterisk (*) in the column after the ID indicates that the set is
defined and managed by the system.
• TAILOR SET GENERAL ATOM_IDENTIFIER to alter the characteristics
of the listings.

Chapter 11.
Use Molecule Databases
• Database Formats on page 158

• Database Tutorial on page 159
• Open and Close SYBYL Databases on page 166
• Retrieve Molecules from a SYBYL Database on page 169
• Obtain Information on Databases on page 173
• Manage Database Content on page 174
• Save Database Molecules to Mol2 Files on page 178
• The DATABASE Command on page 180
• Database Qualifiers on page 179
• System Utilities on page 181

Chapter 11. Use Molecule Databases
Database Formats
11.1 Database Formats

There are currently two different formats for molecule databases:
• mol2dbms—A directory of Mol2 files, containing individual molecules,
and several other utility ASCII files. Often referred to as a Mol2
database. The directory name identifies the database. This format was
introduced in SYBYL 6.1.
• mdbms—A single file, binary format, introduced in SYBYL 5.x.
Note: To explore chemical and biological databases use UNITY, the search and
analysis system. See the UNITY Manual.
Because Mol2 databases are composed of only ASCII files, they are more
portable across different machine platforms than binary databases (e.g., Mol2
databases are portable across platforms, whereas binary databases are not).
Mol2 databases are less susceptible to corruption than binary databases and are
more recoverable in case of corruption, since molecules can be held in separate
files. However, manipulating files within a Mol2 database via the system shell
while the database is open can generate error messages. Closing the database
(and any tables using the database) and reopening it usually eliminates such
errors.
You can create a Mol2 database using the DATABASE CREATE and DATABASE
XCREATE commands, or from the system shell using existing Mol2 files created
by other parts of SYBYL. For example, see the Database Tutorial on page 159.
Also see the TAILOR SET DATABASE command for information about the
MULTIMOL2 variable and how it affects Mol2 databases created from the system
shell.

Database Tutorial
11.2 Database Tutorial

This tutorial describes some of the capabilities developed for the manipulation
of molecule databases. This tutorial demonstrates:
• Adding new molecules to a database.
• Defining sets of molecules in the database. Note: Definition of database
sets is only possible via the DATABASE command.
• Defining relations on these sets.
• Several access methods for looking at the contents of a database.
11.2.1 Set Up
2. Copy a file from the demo directory to your working directory.
¾ cmd cp -r $TA_DEMO/aa.mdb . (include the space and period)
11.2.2 Open the Database

1. Open the database of amino acids and examine its contents.
¾ File > Database > Open
¾ Select aa.mdb and press OK.
¾ Select UPDATE and press OK.
The console reports that the database is open and in UPDATE mode.
Databases can be opened in UPDATE or READONLY mode. If opened in

READONLY mode, any number of users may simultaneously access the
database. On the other hand, no changes can be made to a database unless it is
opened in UPDATE mode.
2. Display a list of the molecules in the amino acid database.
¾ File > Database > List

Database Tutorial
¾ Select MOLECULE and press OK.
¾ Accept * as the Object Name and press OK.
SYBYL displays the names in the console.
11.2.3 Define (Static) Sets of Molecules

1. Enter the DATABASE mode.
¾ In the console, type: MODE DATABASE
Note: The prompt in the console changes to Database command>.
Tip: Use the MODE command for complex commands which have many options.
It allows you to establish the upper level command and only enter options until
you exit this mode. When you are in this mode, any command not available as
an option can be invoked by preceding it with the word COMMAND.
2. Organize the polar amino acids, according to their charge, into sets named
basic, acidic, and polar_neutral. Include a comment string describing the set.
¾ Type the following.

Important: Do not introduce spaces in the list of amino acids for the
Query Expressions.
Database command> DEFINE SET basic
Query Expression<*> lysine,arginine,histidine
Comment String<> Amino acids with positively charged R
groups
Database command> DEFINE SET acidic
Query Expression<*> *acid
Comment String<> Amino acids with negatively charged R
groups
Database command> DEFINE SET polar_neutral
Query Expression<*>
glycine,serine,threonine,cysteine,tyrosine,aspar-
agine,glutamine
Comment String<> Polar amino acids with uncharged R groups
Database sets are user-defined groups of molecules which have some shared
property (or properties). These properties are distinguished from the ones which
Tripos defines (molecule types,…) and database classes. The group membership
of database sets is static.

Database Tutorial
3. Examine the contents of the newly created sets.
¾ SHOW SET *
The definitions of all sets in the current database are shown in the console.
There is no limit on the number of sets.
11.2.4 Define (Dynamic) Classes of Molecules

1. Define two database classes by specifying rules that identify groups of
molecules as hydrophilic or hydrophobic.
¾ Type the following:

Database command> DEFINE CLASS hydrophilic
Query Expression<*> basic+acidic+polar_neutral
Comment String<> Polar amino acids
Database command> DEFINE CLASS hydrophobic
Query Expression<*> ~hydrophilic
Comment String<> Nonpolar amino acids
Important: Database classes are defined by a formula, such as

(basic+acidic+polar_neutral), which is stored as the definition of the group.
Whenever the membership is to be evaluated, it reflects the contents of the
database at that time—not at the moment when the definition was made. In this
way they become dynamic, adapting their contents to the database as it changes.
2. Examine the contents of the classes.
¾ Type: SHOW CLASS *
The definition and contents of all classes in the database are displayed. Notice
how HYDROPHOBIC contains everything that is not HYDROPHILIC (or more
precisely, “not in the property group hydrophilic”).
3. Exit the DATABASE command mode.

¾ Type: ENDMODE
• Define/Modify Definitions of Groups on page 176

Database Tutorial
11.2.5 Build a New Molecule

Add hydroxyproline to the database.
1. Retrieve proline from the database to use as a template.
¾ File > Database > Get Molecule
¾ Select PROLINE and press OK.
2. Label the atoms.
¾ Use on the View toolbar to label the atoms by ID numbers

(Atoms > Atom ID).
3. Add the hydroxyl group.
¾ In the console type: add group oh replace
¾ Click the hydrogen labeled 13.
11.2.6 Add the New Molecule to the Database

Give the molecule its proper name and add it to the database. Molecule names
may be any arbitrary string.
1. Name the new molecule
¾ Click on any atom then Edit > Molecule > Name
¾ In the Name Molecule dialog, enter hydroxyproline and press OK.
¾ Clear the selection.
2. Add hydroxyproline to the database.
¾ File > Database > Put Molecule
The console reports that hydroxyproline is added to the database.

Database Tutorial
11.2.7 Redefine a Set and its Effect on the Class

1. Set the screen to quartered mode.
¾ Use on the Display toolbar to set the screen mode to

Quartered.
2. Since hydroxyproline is an uncharged polar molecule, add it to the

POLAR_NEUTRAL set.
¾ In the console, type the following:

MODE DATABASE
Database command> DEFINE SET polar_neutral
Query Expression<*> polar_neutral+hydroxyproline
¾ Press the Enter key on your keyboard when prompted for a comment
string.
Sets may be redefined at any time, even in terms of their own current contents,
so that it is easy to add a new member.
3. Re-examine the classes.
¾ Type: SHOW CLASS *
Notice that hydroxyproline has been automatically added to the definition of

HYDROPHILIC. Since the class “hydrophilic” was defined in terms of the
groups “acidic”, “polar_neutral”, and “basic”, hydroxyproline automatically
becomes a member of “hydrophilic”.
11.2.8 Search the Database

The next few sections present different ways of accessing database molecules.
The simplest way to retrieve is by molecule name. If you do not know the name,
either at all or exactly, use a wildcard to search the database (by name) for any
matching string. The wildcard (*) alone selects all of the molecules.
¾ Type: SEARCH NAME *
The console displays Select Command<SELECT>.
¾ Press the Enter key.
The console displays Query Expression<*>

Database Tutorial
1. Select leucine from the database.
¾ Type: leucine and press the Enter key.
The console displays Selected Molecule: LEUCINE
¾ In the Molecule Area dialog, select M2 and press OK.
Use the SELECT command with either the molecule’s full or partial name (with
wildcards).
2. Retrieve histidine from the hydrophilic class.
The DATABASE command can use property group definitions as a basis for
generating selection menus. The Standard Fragment Library is organized using
just this feature.
¾ Type: SEARCH MENU Hydrophilic NAME
The following appears in the console:
Hydrophilic
1. basic
2. acidic
3. polar_neutral
Menu items are selected by number. You may move down a level, back up a
level, or go to the top.
¾ Type 1.
Basic
1. ARGININE
2. HISTIDINE
3. LYSINE
¾ Type 2.
¾ Select M3 as the molecule area and press OK.
3. Use an expression to retrieve glutamic acid after first restricting your search to
molecules that are both hydrophilic and acidic.
¾ Type: GET (hydrophilic&acidic)
¾ At the Selection Command<SELECT> prompt, press the Enter key.
¾ At Query Expression<*> prompt, type: glu*
¾ Select M4 as the molecule area and press OK.

Database Tutorial
You can use any combination of union, intersection, difference, and negation of
property groups and name specifications (with or without wildcards) to select
molecules for retrieval. These facilities, coupled with the ability to organize
molecules into groupings meaningful to you, allow arbitrarily complex struc-
tures to be manipulated with ease.
11.2.9 Close the Database

1. Exit the DATABASE command mode.
¾ Type: ENDMODE
2. Close the database.
¾ File > Database > Close
3. This concludes the Database Tutorial.
¾ Use to reset the screen mode to Full.

Open and Close SYBYL Databases
11.3 Open and Close SYBYL Databases

• Open a SYBYL Database on page 166
• Create a New, Empty Database on page 167
• Copy Database Contents to a New Database on page 168
• Define a Database Alias on page 168
• Specify the Default Database on page 168
• Close a SYBYL Database on page 168
11.3.1 Open a SYBYL Database

Notes about Databases:
• The database that is opened becomes the default user database.
• If the database is already open, the access mode of the open database is
changed to the newly specified mode.
• Any number of users may have the same database open READONLY.
However, if one user has a database open in APPEND or UPDATE
mode, nobody else has any access to it until the database is closed. If
one user has a database open in READONLY mode, nobody else is
allowed to open it in APPEND or UPDATE mode.
• SYBYL attempts to assign an alias to the newly opened database using
the base name of the full database name. For example, if the full
database name is /usr/me/mydb.mdb, SYBYL attempts to assign it
the alias “mydb”. This makes using database qualifiers easier. See the
ALIAS subcommand for more information about database aliases.
• TAILOR SET DATABASE to alter characteristics of the database opening.
• To unlock a database that was not properly closed because of a system
crash, enter the following in a console: $TA_BIN/dbunlock
• DATABASE OPEN assigns a value to the UIMS2 variable
DATABASE_NAME.
Via the Menubar
File > Database > Open
The Database Selection dialog that is displayed is very similar to the dialog for
opening files (see the Open File dialog description).

Via the Command Line
User Database: DATABASE OPEN filename access_mode

• filename—Database to open (default extension is
.mdb).
• access_mode—How database is accessed: READONLY,
APPEND, or UPDATE.
System Data- DATABASE SYSTEM system_db access_mode
base: • system_db—Tripos-supplied database that becomes a
“user” database: FRAGMENT_LIBRARY or
GROUP_LIBRARY. (When opened, it becomes the default
database.)
• access_mode—How database is accessed: READONLY,
APPEND, or UPDATE.
Using APPEND or UPDATE prevents others from accessing
the system database, either directly or through FRAGMENT or
ADD GROUP commands, until database is closed.
Note: Care should be exercised when modifying the Tripos-
supplied databases, since much of the program’s operation
depends on their contents.
Create a New, Empty Database
Menubar: File > Database > New

Command Line: DATABASE CREATE filename
filename—Name for database file. Default extension .mdb
is provided automatically.
or: DATABASE XCREATE dbtype filename
• dbtype—Database format: MDBMS or MOL2DBMS.
• filename—Name for database file. Default extension
.mdb is provided automatically.
The database that is created becomes the default user database. It is automati-
cally opened in UPDATE mode; there is no need to open the database after
creation. If a file already exists with the given file name, you have a choice of
replacing the old one or issuing the command again to give another file name.
Replacing the old file creates a new file with that same name and deletes the
contents of the old file.
UIMS2 variable:
• The DATABASE CREATE and DATABASE XCREATE commands assign a
value to the UIMS2 variable DATABASE_NAME.

11.3.2 Copy Database Contents to a New Database

DATABASE TO_MOL2DB source destination
source File specification for the source database.

destination File specification for new database, i.e., the Mol2 database.
If file exists, you can replace the old one or issue the com-
mand again to give another file name. Replacing old file
creates a new file with that same name and contents of old
file are deleted.
11.3.3 Define a Database Alias

DATABASE ALIAS db_name alias
db_name Name or alias of an open user database.

alias New alias.
Aliases are useful in conjunction with database qualifiers. An alias can be used
in a qualifier instead of the full database name. A database can only have one
alias. If the specified database already has an alias, the old alias is overwritten.
A user assigned alias is lost when a user database is closed.
11.3.4 Specify the Default Database
Menubar: File > Database > Default

Command Line: DATABASE DEFAULT db_name
Database operations are applied to the default database if no database is

explicitly specified in a command.
UIMS2 Variable:
• DATABASE_NAME.
11.3.5 Close a SYBYL Database
Menubar: File > Database > Close

Command Line: DATABASE CLOSE
or: DATABASE XCLOSE db_name
If the default database is closed and other databases are open, one is arbitrarily
selected as the new default user database.

Retrieve Molecules from a SYBYL Database
11.4 Retrieve Molecules from a SYBYL Database

11.4.1 Retrieve a Molecule
Menubar: File > Database > Get Molecule

Command Line: DATABASE GET expression [{selection_query}]
[mol_area]
• expression—Database query expression specifying
molecule(s) to retrieve (may include database qualifier,
otherwise default database is assumed).
• selection_query—
ASSIGN—Use SELECT and UNSELECT to specify
molecules to assign.
QUIT—Exit DATABASE GET without loading any
molecules.
RETRIEVE—Retrieve multiple molecules from open
database. To retrieve all molecules in a selection, enter
molecule area for first molecule. Other molecules are
placed in alphabetical order in consecutive work areas.
Previous contents of molecule areas are overwritten.
SELECT—Choose subset of currently selected
molecules. Selection can be a multi-step process.
UNSELECT—Return to set of molecules obtained by last
SELECT command. Can be used as many times as
SELECT.
• mol_area—Molecule area where first (or single)
retrieved molecule is placed (skipped if no molecule
present).
This command behaves differently depending on whether the expression maps

to a single molecule, no molecule, or multiple molecules.
• Single molecule, you are prompted for the molecule area to hold the
molecule.
• No molecules, a message indicates that molecule could not be found.
• Multiple molecules are listed on the terminal and you have access to
additional commands to narrow the selection. Retrieved molecules are
placed in consecutive molecule areas, starting with the one specified
when you entered the command.
• Database Query Expressions on page 170.

11.4.2 Search for Molecule(s) to Retrieve

DATABASE SEARCH search_mode name_expr [action]
search_mode How to search the database:

• NAME—Search by molecule name.
• MENU—Search using menus. The menus provide a
hierarchical structure within databases. The FRAGMENT
command, for example, uses a menu structure to
control searching of the fragment database. Menus are
formed by evaluating molecule groups (sets and
classes). A class which is the union of several groups
appears on a menu listing the component groups. A
group consisting of molecules appears as a menu of
molecule names. Selections continue recursively until
the final molecule is chosen.
name_expr Initial query of the molecule/group name (may include
database qualifier, otherwise default database is assumed).
action Varies depending on the search_mode.
This command is useful for browsing through an unfamiliar database, as well as

for setting up groups which are otherwise difficult to define.
11.4.3 Database Query Expressions

Database query expressions retrieve information about molecules in a database.
The molecules can be retrieved, placed into a group, or simply examined by
name. Molecules can be identified by whole or partial names, by membership in
defined groups, or by a combination of these.
The simplest form of a query expression is a molecule name, which specifies a

single molecule. When specifying a name to retrieve a molecule from the
database, names containing blanks and special characters, such as hyphens or
parentheses must be enclosed in double quotes. Names beginning with letters
and followed by nothing but letters, digits, or underscores may be used without
quotes. This is necessary to distinguish characters in names from operators in
database query expressions.
The next level of complexity in query expressions allows wildcards in molecule

names (but not group names). Finally, operations on groups provide a powerful
technique to designate molecules. They can consist of the logical operators
union, intersection, difference, and negation and the elements to which they are
applied.

The Venn diagrams below illustrate the logical operators. A, B, and C are
general object sets. Shaded areas represent the selected set D which results from
the indicated operations. The outer circle represents the total set from which the
subsets are chosen.
Union Intersection Difference Negation

In either set In both sets In first set and Do not have speci-
not in second fied property
D=A+B or D=A&B D=A-B D=~A
D=A,B
In database query expressions, operators are evaluated from left to right, with
operations of highest precedence evaluated first. The order of operator prece-
dence is (from highest to lowest):
Negation ~ highest
Intersection &
Union, Difference +– lowest
Parentheses group the elements of the expression for evaluation in a specified

order.
Examples
Retrieve tryptophan from current database and place it in M1.
DATABASE GET (tryptophan) m1
Retrieve all molecules whose names begin with t (or T) from current database.
For multiple matches, you are asked to select one.
DATABASE GET (t*) m1
Retrieve all molecules whose names begin with h (or H) and are members of the
group substrate from current database. For multiple matches, you are asked to
select one molecules.
DATABASE GET (substrate & h*) m1
Retrieve all molecules whose names begin with 1,4,5 T and are members of the
group reaction1 or reaction2 (or both). Use parentheses to ensure the union
operation takes place before the intersection.

DATABASE GET (“1,4,5 T*” & (reaction1 + reaction2))
Double quotes around the (partial) molecule name are required since it contains
special characters.
11.4.4 View the Database as a Spreadsheet

The table of data must pertain to the series of molecules from an open user
database. Data can be entered explicitly or calculated from the molecules.
Menubar: File > New > Spreadsheet

Command Line: DATABASE TABLE
• The Molecular Spreadsheet Manual for a complete description.

Obtain Information on Databases
11.5 Obtain Information on Databases

11.5.1 List All Open Databases
DATABASE ALLOPEN
Full database names are listed along with aliases given in parentheses. The
default user database is denoted.
11.5.2 List Contents of an Open Database
Menubar: File > Database > List

Command Line: DATABASE DIRECTORY item_type name_expr
• item_type—ANY, CLASS, MOLECULE, SET.
• name_expr—Expression of names of items to list (may
include database qualifier, otherwise default database is
assumed).
11.5.3 List Molecule and Group Information for an Open Database

DATABASE SHOW item_type name_expr [listing_mode]
item_type ANY, CLASS, MOLECULE, SET.

name_expr Expression specifying names of items to list (may include
database qualifier, otherwise default database is assumed).
listing_mode • BRIEF—Abridged information about selected items,
one-item-per-line.
• FULL—Detailed listing for each item (for ANY or
MOLECULE only).
11.5.4 List Information About an Open Database
Default Database: DATABASE STATUS

Any Open Database: DATABASE XSTATUS db_name
Lists contents, including the database filename, alias, format, access mode and
the number of molecules, sets, and classes currently defined.

Manage Database Content
11.6 Manage Database Content

11.6.1 Add Molecule(s) to a Database
Notes:
• The molecule being added must have a name. (See MODIFY MOLECULE
NAME to give the molecule a name, or Formats for Specifying Objects on
page 202 for syntax of molecule names.)
• The database must be open in UPDATE mode, or APPEND mode is
sufficient if the molecule does not already exist in the database
Menubar: File > Database > Put Molecule

Add to Default DATABASE ADD mol_expr [disposition]
Database via Com- • mol_expr—Expression defining molecules to add to
mand Line: default user database (either a single molecule area
or a comma-separated list of areas).
• disposition—KEEP or REPLACE original molecule.
Add to Database DATABASE XADD db_name mol_expr [disposi-
via Command tion]
Line: • db_name—Name or alias of open user database.
• mol_expr—Expression defining molecules to add
(either a single molecule area or a comma-separated
list of areas).
Name Molecule DATABASE SAVE_AS mol_area new_name [dispo-
and Add to Data- sition]
base via Com- • mol_area—Molecule area containing molecule to
mand Line: save.
• new_name—Name for molecule (may include
database qualifier, otherwise default user database is
assumed).
• Open/Save Mol2 Files via the Command Line on page 41.

11.6.2 Delete Molecule(s) in a Database
Menubar: File > Database > Delete Molecule

Command Line: DATABASE DELETE item_type name_expr NO | YES
• item_type—CLASS, MOLECULE, SET.
• name_expr—Expression of names of items to delete
(may include database qualifier, otherwise default user
database is assumed).
Deletion of groups from a database has no effect on the molecules which were
inside those groups. Molecules themselves must be explicitly deleted.
The database must be open in UPDATE mode for this command to operate
successfully.
11.6.3 Organize Molecules into Groups (Sets and Classes)

• Fragment Library Structure and Contents on page 233
Grouping Mechanisms
Molecules in a database can be organized into groups by the user, providing a

convenient method for representing relationships between molecules. It is
important to recognize the distinction between the sets described below and the
sets of atoms, bonds, or substructures. Here the term “set” is used to refer to a
collection of molecules, not to a particular molecule’s constituents.
Database Sets—A named, static collection of molecules explicitly created
by the user. Examples might be groups called “current_project,”
“substrates,” or “minimized.” Members of a set may be specified by a
database query expression which is evaluated at that time to determine the
members of the set. To update the contents of a set, simply give it a new
definition which incorporates its own value. For example, the following
removes hydroxyproline from the set HYDROPHOBIC.
DATABASE DEFINE SET hydrophobic (hydrophobic-hydrox-
yproline)
Database Classes—Molecules matching a specified database query
expression. Once defined, the class is reevaluated each time it is referenced,
to reflect the current database contents.

Define/Modify Definitions of Groups
DATABASE DEFINE CLASS | SET name expr comment
name Name of the class or set.

expr Database query expression (may include database qualifier, other-
wise default database is assumed).
comment Short descriptive string explaining significance of class/set.
Note:
• Database must be open in UPDATE mode for this command to operate
successfully, or APPEND mode is sufficient if the molecule group does
not already exist in the database.
• Each time a defined class’ name appears in a database query expression,
it is reevaluated and its members determined for the database.
• If a molecule, defined as a member of a set, is deleted, that molecule is
automatically removed from the set.
• The Database Tutorial on page 159 for an example.
Rename a Group or Molecule
Menubar: File > Database > Rename Molecule

Command Line: DATABASE RENAME item old_name new_name
• item—CLASS, MOLECULE, SET.
• old_name—Current name of group or molecule.
• new_name—New name for group or molecule.
Notes:
• If new_name for a molecule already exists in the database, you are asked
whether or not the new molecule should replace the current one.
• If new_name for a group already exists in the database, the operation
fails.
• Database must be open in UPDATE mode for this command to operate
successfully.
• Both names may contain a database qualifier. However, the operation
fails if the qualifiers do not refer to the same database.

Reorganize and Compress Database Contents
DATABASE REORGANIZE filename
filename Name of the database file (default extension is .mdb).
Reorganizing and compressing the contents of a molecule database allows

unused space to be reclaimed.
mol2dbms:
• Mol2 files containing more than one molecule are broken into multiple
Mol2 files, one molecule per Mol2 file. This “flattens” the database.
• Mol2 files are renamed so file name matches (or nearly matches) name
of molecule in file.
• Reorganization can decrease access time, but has little effect on database
size, since Mol2 databases rarely accrue unused space.
• Reorganizing a Mol2 database is useful only when the database was
created by the user directly from the system shell. This is because Mol2
databases, created and accessed only via the DATABASE command, have
neither MultiMol2 files nor misnamed Mol2 files.
• Whenever SYBYL writes Mol2 files via the DATABASE command(s),
they are written with at least 6 digits of precision. If the value of the
tailor variable MOL COORD_PLACES is less than 6 (such as the default of
4), it is set to 6 during the operation of the DATABASE command and
reset when complete. If, however, the values higher than 6, the tailor’s
value is used throughout.
• Warning: The DATABASE REORGANIZE command creates a new Mol2
database with a temporary name. This name is generated in the directory
set by the environment variable TMPDIR. If the variable is not set, the
new database is created in the working directory. If this variable is
defined in your environment, that is where the new database ends up,
and hence appears to be lost.
mdbms:
• A consistency check ensures the database contents match the index
structure. This is the only accepted method of recovery for a corrupted
database (as indicated by the error message RECORD_KEY_ERROR).
• Database must not be open by any user when the REORGANIZE command
is given. The reorganized database overwrites the old file.
• Highly active databases should be periodically reorganized to recover
unused space. Compressing the files can have a significant impact on
access time.

Save Database Molecules to Mol2 Files
11.7 Save Database Molecules to Mol2 Files

Menubar: File > Database > Write MOL2 File
Command DATABASE WRITE_FILE2 expression selection_query
Line: [filename]
• expression—Molecule(s) to write out to file(s) (may
include database qualifier, otherwise default database is
assumed). Multiple molecules are listed in console.
• selection_query:
SELECT expr—Available if multiple molecules are
specified. Choose a subset of molecules. Expression
provided here is limited to currently specified molecules,
even though other database molecules might match.
Selection continues until either OUTPUT or QUIT is chosen.
UNSELECT—Available if multiple molecules are specified.
Return to set of molecules obtained by last SELECT
command. UNSELECT can be entered as many times as
SELECT was used to narrow the selection.
OUTPUT—Write selected set of molecules to file.
QUIT—Exit command without writing the file.
• filename—File to hold molecules (default extension is
.mol2). This argument is skipped if QUIT is entered.
Note: Mol2 files written via database operations have at least 6 digits of
precision. If the tailor variable MOL COORD_PLACES is set to < 6 (such as the
default of 4), it is set to 6 during the operation of the DATABASE command and
reset when complete. If the value is > 6, the tailor’s value is used throughout.

Database Qualifiers
11.8 Database Qualifiers

A database qualifier is added to a query expression to explicitly specify the
database to which the expression applies. It consists of a database name (or
alias) placed before the query expression, separated from the query by the “!”
character. A query expression without a database qualifier automatically applies
to the default user database.
SYBYL first checks the names of open databases (which can be seen using the
ALLOPEN command). If the database qualifier matches a name of an open
database, that database is selected for the operation. If no open database name
matches, then the SYBYL checks the alias of any open database. If there is a
match, that database is selected for the operation. If no aliases of open databases
match, then the qualifier is considered to be invalid. (The same process applies
to the open database arguments of the ALIAS, DEFAULT, XADD, XCLOSE, and
XSTATUS subcommands.)
Note: Double quotes must be used when spaces occur in a database qualifier.
Also, if the special character “!” occurs in a molecule name, the molecule name
should be enclosed in double quotes.
Examples
Retrieve tryptophan from the default database and place it in M1. (No database
qualifier is needed.)
DATABASE GET (tryptophan) m1
Retrieve all molecules whose names begin with t (or T) from the database /usr/
me/mydb.mdb. For multiple matches, select one.
DATABASE GET /usr/me/mydb.mdb!(t*) m1
Retrieve the molecule named botulin from the database whose alias is toxins
and place it in M3. (A database such as /usr/me/project_xyz/toxins.mdb is
automatically assigned the alias toxins when opened.)
DATABASE GET toxins!botulin m3
See the OPEN and ALIAS subcommands for additional information about
database aliases.

The DATABASE Command
11.9 The DATABASE Command

The DATABASE command provides functionality to manipulate molecule
databases, whether they have been supplied by Tripos or defined by the user.
DATABASE functions can be accessed in two ways:

• Precede each subcommand with the word DATABASE.
• Type MODE DATABASE to enter the DATABASE mode. To exit this mode,
type either the end-loop character (|) or ENDMODE. Selecting another
menu category also exits the DATABASE mode. When in DATABASE
mode, other SYBYL commands can be accessed by preceding them with
COMMAND.
Below is a list of the DATABASE subcommands:
ADD ENDMODE SYSTEM

ALIAS GET TABLE
ALLOPEN MATCH_ALIGN TO_MOL2DB
(QSAR Manual)
CLOSE OPEN WRITE_FILE
COMMAND RENAME WRITE_FILE2
CREATE REORGANIZE XADD
DEFAULT SAVE_AS XCLOSE
DEFINE SEARCH XCREATE
DELETE SHOW XSTATUS
DIRECTORY STATUS

System Utilities
11.10 System Utilities

Since system commands like rm and cp behave differently when operating on
regular files versus directories (without additional flags), the following system
shell scripts are provided in $TA_BIN.
• db_rm removes molecular databases of either format:
db_rm db1 ... dbN
• db_cp copies a molecular database of either format:
db_cp source_db target_db
The format of target_db is the same as that of source_db. target_db is

overwritten if it already exists.

Chapter 12.
Manage SYBYL Sessions
• Save a SYBYL Session on page 184

• What is Saved in a Session?
• What is Not Saved in a Session?
• Details About Saved Backgrounds
• Open (Restore) a Saved Session on page 189
• Delete a Saved Session on page 189
• Open a New Session on page 189
• Close a SYBYL Session on page 190
• Record and Play Back SYBYL Operations on page 191
• Record SYBYL Operations in a File
• Play Back a File of Recorded Operations
• Insert a Pause in a Recorded File
• Read Command Input From a Text File
• Record the Output from a Single Command
• Record the Console Dialogue of a Session

Chapter 12. Manage SYBYL Sessions
Save a SYBYL Session
12.1 Save a SYBYL Session

A SYBYL session, in its current state, can be saved in a specified directory.
This allows you to return to SYBYL at a later date and continue your work from
the point where you saved the session. See Open (Restore) a Saved Session on
page 189.
Save the Session
Menubar: File > Save Session (Ctrl+S)

Or File > Save Session As
Icon:
or on the Standard toolbar.
Command Line: SESSION SAVE dir_name
Each SYBYL session is saved in a directory. The default name for a session
directory is the current date and time (dd_mmm_yyyy_hh_mm). The extension
.ses is appended automatically. Saving a session changes the default directory
to that of the saved session.
The first Save Session ( )operation prompts for a directory name. Subse-
quent Save Session operations for the same session, whether newly created or
restored from a previously saved session, overwrite the same directory.
Use Save Session As ( ) to save the current session to a new directory.
Save the Session and Exit SYBYL
Command Line: SESSION SQUIT dir_name
To specify a single default location (other than “current working directory”),
use the environment variable SAVE_SESSION_DIR, which must be set prior to
starting SYBYL.

12.1.1 What is Saved in a Session?

A SYBYL session is a directory of files that contain the full specification
necessary to restore the session at a later time. For that purpose the following
are saved.
• All molecules in their displayed state are saved to individual .mol2 files
that include for all atoms their show/hidden status, color, labels, and
rendering mode.
• Data necessary to preserve rotatable bond angles and to restore dynamic
hydrogen bonds, distance and bump monitoring.
• Surfaces and ribbons associated with molecules as well as their show/
hidden status and color.
• Toolbars: position of all toolbars, visible status of all icons, user-defined
icons.
• Screen settings:
• Global and individual rotations and translations as well as scale
• Screen mode: full, quartered, etc.
• View mode: mono, orthographic, relaxed, and crossed stereo, (but
not stereo in a window) and associated settings
• Depth cue and Z-clipping
• Font, color and lighting
• Tailor variables and parameter files (.tpd)
• Tables based on:
• Molecule databases (including analyses).
• UNITY hitlists
• MDL SD/RD files
• Dynamics history files
• Conformational search angle files
• Imported data
Also saved with tables are analyses and supporting files for CoMFA,
EVA, and CoMSIA columns. If the row labels are 2D structures when
saved, then restoring also shows these labels.
• The following types of background objects:
• Rulers
• MOLCAD surfaces
• Protein rendering

• Biopolymer ribbon
• Hbond
• Multiple volume surfaces
• Potential
• Dots
• QSAR contours
12.1.2 What is Not Saved in a Session?

• Table graphs
• Tables based on:
• UNITY database
• Biopolymer loop search
• ProTable
• Backgrounds not supported:
• Generalized Surfaces
• Isosurfaces
• Contour display created surfaces-CoMFA region
• MOPAC
• AMPAC
• Force Field constraints
• Annotations
12.1.3 Details About Saved Backgrounds

MOLCAD Surfaces
• The surface style (lines, dots, etc.) and the current coloring property are
retained.
• If the color of a MOLCAD surface is changed with the BACKGROUND
COLOR command, the color will not be restored correctly.
Protein Rendering
• The following settings are taken from the time of creation:
• The opaque/transparency (TAILOR!RENDER!SURFACE_TYPE)
• Display of alpha helices (TAILOR!RENDER!HELIX_DISPLAY)

• Determination of secondary structure elements

(TAILOR!RENDER!SEC_STR_SRC)
• All other settings of TAILOR!RENDER are taken from the tailor.save
file at the time of the session saving:
• If the coloring is by table column, it will not be retained.
Biopolymer Ribbon
• The number of strands and color are retained.
• Setting for TAILOR!RIBBON!RIBBON_WIDTH is taken from the
tailor.save file at the time of the session saving.
Hydrogen Bonds
• The atom set and color are retained.
• All settings of TAILOR!HBONDS are taken from the tailor.save file at
the time of the session saving.
• The .dsp file is not saved, as the background will be recreated upon
restoration of the session.
QSAR Contours
• The graph field file must be saved during the contour creation. This file
is saved if the contour was created from the QSAR GRAPH FIELD
command. If the View CoMFA dialog was used, the Save to File(s)
check box must be on.
• The surface type used at creation is retained using the
TAILOR!CONTOUR!DISPLAY_AS setting.
• All TAILOR!TABLE and TAILOR!GRAPHS values are taken from the
tailor.save file at the time of the session saving.
• The .dsp and .cnt files are not saved, as the background will be
recreated upon restoration of the session.
Volume/Mvolume
• The volume color and surface type used at creation are retained using the
• Settings of TAILOR!VOLUME are taken from the tailor.save file at the
time of the session saving. However, volumes created with
TAILOR!VOLUME!MAP_RANGE set to FIXED_RANGE are not restorable.

• The filename originally used to create the .dsp/.cnt file is not retained.
A default name is used to guarantee that more than one of these surface
types can be restored without needing to prompt the user.
Potential
• The surface type used at creation is retained using the
• Settings of TAILOR!POTENTIAL are taken from the tailor.save file at
the time of the session saving.
• The filename originally used to create the .dsp/.cnt file is not retained.
A default name is used to guarantee that more than one of these surface
• These backgrounds are not restorable with TERM NO.
Dots
• The coloring method used at creation is retained.
• Settings of TAILOR!DOTS are taken from the tailor.save file at the time
of the session saving.
• The .dot file is not saved, as the background will be recreated upon
restoration of the session.
• The filename originally used to create the .dot file is not retained. A
default name is used to guarantee that more than one of these surface

Open (Restore) a Saved Session
12.2 Open (Restore) a Saved Session

Previously saved SYBYL sessions can be restored using either of the following.
Menubar: File > Open Session (Ctrl+O)

The 5 most recent sessions are listed on the File menu
in reverse chronological order.
Icon:
on the Standard toolbar.
Command Line: SESSION RESTORE dir_name
Each saved SYBYL session is stored in a directory with the .ses extension. See
Save a SYBYL Session on page 184.
During restoration:
• The current working directory is changed to the location of the restored
session’s directory.
• Prompts are also presented regarding the deletion of any currently
displayed molecules, backgrounds, and tables before continuing.
12.3 Delete a Saved Session

To delete a saved session simply delete the session directory.
12.4 Open a New Session

Open a new SYBYL window where you can perform work independently of the
current session.
Menubar: File > New > Session (Ctrl+N)

Icon:
on the Standard toolbar.
If licensing does not allow for an additional SYBYL window a dialog will
inform you that the session limit has been reached.
See License Requirements for SYBYL Basics on page 8.

Close a SYBYL Session
12.5 Close a SYBYL Session

If you have multiple SYBYL sessions open simultaneously you must close each
of them individually.
File > Close Session
When closing a SYBYL session you will be prompted whether to save it s
Closing a session performs the following operations:

• Prompts whether to save the current session so that the current state of
SYBYL reloaded at a later time. See Manage SYBYL Sessions on page
183 for more details.
• Deletes all molecules and background objects (Edit > Delete Every-
thing).
• Closes all spreadsheets and associated databases.
• Reset the directory that the default when SYBYL was launched.
Closing a session does not exit SYBYL.

Record and Play Back SYBYL Operations
12.6 Record and Play Back SYBYL Operations

SYBYL includes scripts for tracking commands and playing back recorded
operations. These are useful for documenting a session and when tracking
potential problems in the use of SYBYL. It is important to activate these
options at the beginning of your SYBYL session.
A collect/take file consists of a series of command lines where each command

must appear on a single logical line. Lines are terminated by an end-loop
character (|) unless the last character on the line is a back slash (\).
The following characters, when first on one line, have special meaning in a
collect file:
# ignore the line, typically used for comments,
% if current session is interactive ask user for confirmation before
continuing, typically used to pause during playback.
• Automatic Command Execution at SYBYL Startup on page 238
12.6.1 Record SYBYL Operations in a File

When this option is enabled, all commands and arguments are captured into a
file which can be replayed to reproduce a session. The file closes automatically
at the end of the SYBYL session.
Menubar: Options > Record Macro

Command Line: COLLECT action [filename]
• action:
APPEND—Reopen existing file and continue journaling.
COMMAND—Force collection of next command even if
collection was suspended.
FILTER—ON/OFF; whether to collect all SPL
constructs.
FORCE_RESUME—Resume journaling even if multiple
SUSPEND commands were made.
ON—Enable journaling of command input in file.
OFF—Stop journaling of commands and close file.
RESUME—Cancel last SUSPEND.
SUSPEND—Temporarily suspend journaling without
closing file.
• filename—File to receive journaled commands. Default
extension is .col.

To store actions of menu picks in a collect file, first issue the command MENU
COLLECT ON.
Only one COLLECT file can be open at a given time.
UIMS2 Variable:
• UIMS2_COLLECT_FILE—Name of the current collect file.
• Record the Console Dialogue of a Session on page 194
• Read Command Input From a Text File on page 193
• Insert a Pause in a Recorded File on page 193
• Play Back a File of Recorded Operations on page 192
12.6.2 Play Back a File of Recorded Operations

A recorded session can be used to repeat a series of commands on several
different molecules, to replay a demonstration script, or to recover one’s
position lost as a result of system failure.
Menubar: Options > Load Macro

Command Line: TAKE filename
When an incomplete command line is encountered in the file, interactive

prompting takes place to finish the command before proceeding to the next
command line.
• Record SYBYL Operations in a File on page 191
• Read Command Input From a Text File on page 193
• Insert a Pause in a Recorded File on page 193

12.6.3 Insert a Pause in a Recorded File

PAUSE delta_time
delta_time Number of seconds to pause program execution.
By inserting this command into the recorded session file, you can halt program
execution for a specified number of seconds or indefinitely, if delta_time is set
to zero. In this way, you can give the user ample time to read the comments.
PAUSE is used in preparation of demonstration scripts. Note: These scripts
cannot be played back in menu mode.
As an alternative to PAUSE, inserting the WAIT command suspends execution

until either C (continue), G (go), or Q (quit) is entered. Enter either command at
the keyboard during the recording session or edit the file afterwards.
• Record SYBYL Operations in a File on page 191 to prepare a script.
• Play Back a File of Recorded Operations on page 192 to play back a
prepared script.
12.6.4 Read Command Input From a Text File

TTY filename
Input is read from the specified file (file extension must be included) until an
end-of-file condition is encountered. The text in the file is executed as if it was
manually entered by the keyboard. This is convenient when generating
command procedures without the use of the COLLECT command. (The tutorial
files (.demo) have this format.)
Warning:
TTY does not understand command context as does the TAKE command. Thus
any mistakes in the TTY file are faithfully executed.

12.6.5 Record the Output from a Single Command

The text output from a single command can be sent to a file. This is useful for
storing lengthy output of commands such as minimizers, LIST, TOPOGRAPHY,
etc.
CAPTURE filename command
filename File to receive output generated by specified com-

mand. No default file extension.
command A single SYBYL command with all its arguments.
• List Coordinates, Distances, or Angles on page 149.
• List Information About SYBYL Objects on page 155
12.6.6 Record the Console Dialogue of a Session

When this option is enabled, the complete dialogue is recorded in a file.
Program prompts, user responses, commands, and program output are recorded
in this file. It can be used to document sessions with the program as an adjunct
to a laboratory notebook. The file closes automatically at the end of the SYBYL
session.
Menubar: Options > Log Session

Command Line: PHOTO status [filename]
• status:
ON—Record console dialogue to specified file. Infor-
mation is first stored in a buffer. By default, buffer is
automatically flushed to the file as soon as it is full.
OFF—Terminate recording.
FLUSH—Write all currently buffered PHOTO infor-
mation immediately to file. Future I/O flushing is not
affected by this command.
LINEBUFFER—Line buffer pending and all future
PHOTO I/O, data is flushed continuously to file. LINEB-
UFFER is off initially. If you turn PHOTO OFF then back
ON, you must explicitly turn on LINEBUFFER again.
• filename—File to receive the console dialogue. There is
no default extension.

UIMS2 Variable:
• UIMS2_PHOTO_FILE—Name of the current photo file.
• Record the Output from a Single Command on page 194

Chapter 13.
SYBYL Objects and Their Expressions
• Definitions of SYBYL Objects on page 198

• Formats for Specifying Objects on page 202
• Naming Rules and Special Characters in Expressions on page 202
• Substructure Specification on page 206
• Set Specification on page 207
• Molecule Specification on page 207
• Molecule Area Specification on page 207
• Conformational Specifications on page 210
• Create Complex Expressions on page 211

Chapter 13. SYBYL Objects and Their Expressions
Definitions of SYBYL Objects
13.1 Definitions of SYBYL Objects

Molecule Areas
Work spaces which hold structures being manipulated. Areas are designated by
the letter M followed by an integer. Any number of molecule areas can be
defined at any time, since SYBYL can handle an unlimited number of
molecules simultaneously. They may be assigned in arbitrary order, and will
hold any named entity supplied either from an external file, through
construction internally, or from a database. A molecule area may contain a
single atom, multiple fragments, water molecules, ions, or other components,
and structures with unfilled valences.
Atoms
The fundamental building blocks of molecules. You may name them arbitrarily
and specify their type. Parameters for over 50 different atom types are provided
in SYBYL. An extended list of more than 103 atom types is available in the file
$TA_DEMO/metals.tpd. You can easily expand this number by adding new
types of your own. Atoms can exist as bonded entities or singly.
Bonds
Connection between atoms to form molecules. Bond types (single, double,
triple, amide, aromatic, dummy, or non-chemical) are determined by the types
of atoms they join. Bond types determined automatically by the program can be
overridden to accommodate exceptional circumstances in a particular molecule.
Substructures
Group of atoms in which it is possible to reach any atom from any other atom
along a bonded pathway. No atom in a molecule can belong to more than one
substructure. A substructure may be a single atom, molecule fragments,
functional groups, or monomers in a polymer. They are included in the molecular
description to help subdivide problems into manageable sizes and easily reference
pieces of the molecule.
Substructures are created and managed by SYBYL without intervention. For

example, when constructing a biopolymer from monomers defined in a
dictionary or reading one in from a standard biopolymer structural file such as
the Protein Data Bank, each residue is a substructure. An example of the
substructure assignment for a short peptide sequence is shown below
(substructure boundaries marked by parentheses).

In the case of non-polymers, the only control you have over the creation and
designation of substructures is in the order you construct the molecules or in
fragments chosen from the standard fragment library. All fragments in the
fragment library are designated as substructures. There is no unique assignment
of substructures to molecules. One person might assign them differently from
another. For example, the figure below shows two copies of a single molecule
which have been partitioned differently into substructures. Neither one is neces-
sarily a better choice than the other; they are merely different.
Features
Features are molecular characteristics. They can be based on atoms, other
features, or contain other information.
• Center of mass, centroid, extension point, line, normal, plane, and
various UNITY features
• Force field angle, distance, range, periodic boundary conditions and
torsional constraints
• Sets, including aggregates

• Search anchor atom, rotatable bonds, ring closure and distance

constraints
• Crysin unit cell parameters and space group
• Associated data file locations
• Associated dictionaries
• Alternate atom types
Rings
SYBYL detects the formation and records the presence of rings at all times in
all molecules. Rings have wide-ranging implications for conformational manip-
ulations as well as modification of internal parameters, such as bond lengths and
angles, and they play an important role in identifying similarities among
molecules.
• Internal ring—A ring completely contained within a substructure.
Atoms and bonds in an internal ring are distinguished by the character *
next to their name in the atom or bond list.
• External ring—A ring which spans substructure boundaries. Typically
occur in polymers which are cross-linked (e.g., a peptide structure which
has one or more disulfide bridges). Atoms and bonds in an external ring
are distinguished by the character @.
The figure below illustrates both internal and external rings. The boxes
delineate substructure (monomer) boundaries in this peptide fragment. The
phenyl group in the phenylalanine monomer is an internal ring since it occurs
completely within the confines of a substructure. The heavy, dark bonds
indicate a ring formed by the cross-linking of the peptide by a disulfide bridge
between two cysteine monomers. It is termed an external ring because it crosses
substructure boundaries.

Sets
Named collections of objects substructures, atoms or bonds used for identifying
and naming important groups in a molecule. A set can be used as a shorthand
notation for groups of atoms, bonds, or substructures which are referenced
often.
• Static sets—Membership is identified at the time of definition. Once
specified, this membership does not change unless one of the elements
(atoms, bonds, substructures) is deleted from the molecule. For example,
identify the amino acids in the active site of an enzyme and name them
for quick access.
• Dynamic sets—Membership is defined in terms of a rule and evaluated
at the time of reference. For example, the environment around a
particular atom in a molecule can be defined as a set using a sphere of
specified radius. As the molecule’s conformation is manipulated, the
membership in the set may change. When you reference this set’s name,
the contents of the volume are identified by evaluating the rule at that
time. The built-in sets in SYBYL are dynamic sets: Aromatic, H-bonds,
Backbone, Sidechain, Rings, Bumps, and Metals.
See Sets in SYBYL on page 215 for more details.

Formats for Specifying Objects
13.2 Formats for Specifying Objects

13.2.1 Naming Rules and Special Characters in Expressions
There are a number of general naming conventions and special symbols used to
denote the various objects in SYBYL.
Molecules Names can be arbitrarily long and complex, containing any

characters (alphanumeric, underscore,...). Enclose name in
double quotes (“ ”) if it starts with a numeric character, has
special characters, or a space.
Atoms, Sub- No limit on the number of characters in a name. Tripos rec-
structures, ommends 7 characters for atoms and substructures, and 31
Sets, Features for sets and features. Names must start with an alphabetic
character, but are case insensitive (characters are held inter-
nally in uppercase). Names may contain digits, underscores
(_), and apostrophes (') in any position after the first.
• CA CA12—Valid atom names
• 1C C(1)—Invalid atom names
Note: Only set names are required to be unique.
Chains Names are restricted to 4 characters and must start with an
alphanumeric character. If the name begins with an alpha-
betic character, the following characters can be A-Z, 0-9, _, $
or '. If the name begins with a numeric character, the follow-
ing characters must also be numeric. They may contain
underscores in any position after the first position and before
the last position.
* Match any number of characters of any type.
@ Match a single character of any type.
In addition to the conventions listed above, there are object-specific protocols.

These are discussed in the following sections:
• Substructure Specification on page 206
• Set Specification on page 207
• Molecule Specification on page 207
• Molecule Area Specification on page 207
• Conformational Specifications on page 210

• Add Molecule(s) to a Database on page 174 for adding molecules to a
database.
13.2.2 How to Specify an Atom Expression

Many SYBYL commands operate on a specified group of atoms represented as
atom_expr in the command descriptions.
To supply an atom or group of atoms in a written expression, use any or a

combination of the following methods.
Specify by: Notes and Examples:

Atom ID Atom ID numbers.
Atom Name HIS1.CA—CA atom in residue HIS1.
HIS1.*—All atoms in substructure HIS1.*.
*.CA—All atoms named CA in all substructures.
*—All atoms in default molecule area.
A*.C1—All atoms named C1 in substructures whose name
begins with A.
Atom Type <N.2>—All sp2 nitrogens.
<O.*>—All oxygens (equivalent to O).
<C*>—All carbons, plus any atom type beginning with a C
(e.g., calcium, chlorine, etc.).
Notes:
• Types are case insensitive. The modifier identifies different
forms of the same element (not necessarily hybridization
states).
• See the Force Field Manual for a list of predefined SYBYL
atom types.
Molecule M1—All atoms in molecule area 1.
Area M2(atom_expr)—The atoms in M2 identified by the atom
expression.

Substructure {PHENYL}—All atoms in substructure(s) named PHENYL.

and Set {5}—All atoms in substructure with group ID 5.
{HELIX}—All atoms in set named HELIX.
{HYDROPHOBIC}—All atoms in set named HYDROPHOBIC.
{HIS*}—All atoms in all histidine residues (same as {HIS*}).
{SPHERE(PHE20.CA, 10.5)}—All atoms in 10.5 Å sphere
around the α-carbon of residue PHE-20.
Notes:
• Substructures are searched first for name matches, then, if
none match, all forms of both local and global sets are
searched. Only sets with atoms as objects are valid.
• For biopolymers, a number in braces indicates the sequence
number, which may differ from the substructure ID.
Connected C1:C10—All atoms on all paths from C1 to C10, inclusive.
Path 5:8—All atoms on all paths from atom 5 to atom 8, inclusive.
Notes:
• If rings are in the path, all paths through the rings are
searched.
• Connected paths where the endpoint atoms are members of
rings are ambiguous and may not produce the desired
selections.
Substructure {PHE10:HIS25}—All atoms in all monomers of a biopolymer
Path chain from PHE10 to HIS25, inclusive.
{1:10}—All atoms in all monomers of a chain from residue 1
to 10, inclusive.
Notes:
• Braces ({}) identify all atoms in the substructures on the
path, not just atoms in the bonded pathway.
• Only monomers on the direct backbone path between the
first and second monomer are identified, even in the
presence of rings.
• Sets are not defined in terms of connectivity, only the
substructure name list is searched for matches to determine
the origin and targets of the scan.
Chain A/HIS1.CA—CA atom in residue HIS1 of chain A.
Note: Only one chain specification per expression. Chain spec-
ification cannot be combined with single or range ID numbers
because IDs constitute unique identifiers.
• Naming Rules and Special Characters in Expressions on page 202.

13.2.3 How to Specify a Bond Expression

Several SYBYL commands operate on a specified group of bonds represented
as bond_expr in the command descriptions.
To supply a bond or group of bonds in a written expression, use any or a combi-

nation of the following methods.
Bond ID Bond ID numbers.

Atom Name CA—All bonds connected to the CA atom(s).
O*—All bonds to atoms whose name starts with an O.
Note: Name one or both endpoint atoms.
Bonds Type <2>—All double bonds.
<AR>—All aromatic bonds.
Note: SYBYL bond types are: single <1>, double <2>, triple
<3>, aromatic <AR>, and amide <AM>.
Molecule M1—All bonds in molecule area 1.
Area M2(bond_expr)—The bonds in M2 identified by the bond
expression.
Substructure {MONTYPE(TYR)}—All bonds in substructure(s)/monomer(s)
and Set of type tyrosine.
{5}—All bonds in substructure with group ID 5.
Note: Substructures are searched first for name matches, then,
if none match, all forms of both local and global sets, are
searched. Only sets with bonds as objects are valid.
Substructure {PHE10:HIS25}—All bonds in all monomers of a biopolymer
Path chain from PHE10 to HIS25, inclusive.
{1:10}—All bonds in all monomers of a chain from residue
number 1 to residue 10, inclusive.
Notes:
• Braces ({}) identify all atoms in the substructures on the
path, not just atoms in the bonded pathway.
• Only monomers on the direct backbone path between the
first and second monomer are identified, even in the
presence of rings.
• Sets are not defined in terms of connectivity, only the
substructure name list is searched for matches to determine
the origin and targets of the scan.
Chain A/HIS1.CA—Bonds involving CA atom in residue HIS1 of
chain A.

Specific C1=C10—Bond between atoms C1 and C10.

Bond HIS1.CA=HIS1.CB—Bond between alpha (CA) and beta (CB)
carbons in residue HIS1. In this case, endpoint atoms must be
unique. This technique can only be used to designate one
unique bond.
3=7—Bond between atoms whose IDs are 3 and 7.
Note: Atoms must be bonded directly to one another.
13.2.4 Substructure Specification

Substructure specification can be accomplished using several mechanisms
discussed in the following table.
Note: Enclosing a substructure’s name or ID in braces ({}) is only required

when specifying the name of a set to select the substructures of interest. This
forces both the substructure name list and set name list to be searched for
matches with the input name. Otherwise, only the substructure name list is
searched.
ID Number For biopolymers, ID refers to monomer sequence (e.g. 15 in

ALA15).
For small molecules, ID refers to substructure ID.
A hash or pound sign (#) preceding a number is interpreted as
a substructure ID, even for biopolymers.
Substructure {RING*} or RING*—All substructures whose name starts
Name with RING.
Note: The name must start with an alphabetic character. Digits,
underscores, or apostrophes may follow.
Substructure {PHE10:HIS25}
Path • In biopolymer, all monomers along direct backbone path
from PHE10 to HIS25.
• In small molecule or sequence numbers, all substructures
on all paths from PHE10 to HIS25.
Chain A/ALA15—Substructure with name of ALA15 in chain A.

Set Name {MONTYPE(ALA)}—All substructures that are monomers of

type alanine. MONTYPE is a built-in set.
Note: Only sets with substructures as objects are valid and
appear on the menu.
13.2.5 Set Specification

Braces ({}) are not necessary for set designation, but are accepted for consis-
tency (e.g., RING_A {HELIX_*})
13.2.6 Molecule Specification

A molecule’s full name, or a fraction thereof, and the wild character (*) can be
used. Enclose names that start with a numeric character, contain special
characters, or a space, in double quotes.
”alpha_chymotryp“
”active isome #3“
”5HT“
13.2.7 Molecule Area Specification

The default molecule area is the one in which you are normally performing all
operations. To perform operations on another molecule without changing the
default area (e.g., to measure intermolecular distances), specify the molecule
area before the expression, which is enclosed in parentheses:
M2(C3)
This example specifies all atoms named C3 in molecule area M2.
The molecule area name (M#) associated with a molecule remains the same
during a session.

13.2.8 Monomer Sequence Specification

Monomer sequence specifications can be divided into two categories, generic
and specific (refer to the Sequence Expression dialog for making your selection
with the mouse).
Generic Monomer Sequences
A generic monomer sequence is a list of monomer names connected by an equal

sign (=). Monomer names may be given as the normal monomer name (1 to 4
characters long), or as the one character code, as defined in the macromol
dictionary.
gly=ala=phe
e=p=f
The sequence may contain numerical repeat counts to indicate repetition of a

sequence (the sequence to be repeated must be enclosed in parentheses).
2(arg)=val=phe=3(ser=cys)
is equivalent to:
arg=arg=val=phe=ser=cys=ser=cys=ser=cys
and also equivalent to:
arg=arg=val=3(ser=cys)
Specific Monomer Sequences
A specific monomer sequence is a sequence in the default molecule area. The

following forms are allowed:
mon=mon=mon= Connected linear sequence of monomers. * in

place of a monomer matches any monomer.
mon:mon:mon: Guided range of monomers. All monomers on a
direct path along the backbone of the biopolymer
between adjacent monomers are selected.
* The entire biopolymer.
molecule area(sequence) Sequence in stated molecule area.
“mon” may be:

• General monomer name matching any monomer of that type (e.g. phe)
• Specific monomer name detected by the presence of digits and matching
only a monomer with that exact name (e.g. phe27)
• Sequence number matching any monomer with that sequence number as
part of its name (e.g. 18)

• The < or > character matching the beginning and ending monomers of a
chain, respectively.
Note that monomer names, as defined in the dictionary, may not contain digits,
and each monomer in a molecule should contain a sequence number in its name
(usually indicating its position in the chain).
Sequence specifications can be combined by separating them with commas. To

specify a sequence on a particular chain of the biopolymer, prefix the specifi-
cation with the chain name followed by a slash (e.g. A/*). To specify a
sequence in a molecule area other than the default area, enclose the entire speci-
fication in parentheses, and prefix it with the molecule area (e.g. M3(glu3)).
As an example, consider the nucleic acid fragment:

a1=c2=g3=g4=u5=a6=c7=a8=g9
Entering this: Selects this:

g3:a6 g3=g4=u5=a6
a=c a1=c2, a6=c7
6:8 a6=c7=a8
* a1=c2=g3=g4=u5=a6=c7=a8=g9
c=*=g c2=g3=g4, c7=a8=g9
u,a1=c2 u5, a1=c2
7:> c7=a8=g9
A number refers to the monomer with that sequence number as part of its name
(e.g. 8 in GLY8). As a special case, to identify the monomer by its substructure
ID number, precede the ID number with a hash or pound sign (#). This is partic-
ularly useful when dealing with unresolved ends of protein chains.
• Built-in Sets on page 223

13.2.9 Conformational Specifications

This type of data specification dictates the conformation of all or part of a
biopolymer. Conformational state names, or conformational angle names with
the angle value (in degrees) are both acceptable. Conformational states and
angles are defined in the dictionary. (Note: Only the minimum number of initial
characters of the name required to distinguish it from other conformational
states or angle names needs to be typed.)
Separate multiple specifications with commas. The formats for conformational

specifications are as follows:
• statename—Assigns angle values as defined in the given state.
• angle1=xxx,angle2=yyy—Alters the present angles to the specified
values.
Examples:
alpha_helix
alph
phi=-58.0,psi=-47.0
staggered,beta=120
The valid state names are given in the following table.
alpha_helix none three/10_helix

aturn pi_helix trans
beta_sheet random trans6
b_like random_12 turnI
c5 random_13 turnII
c7ax random_14 turnIII
c7eq random_16 turnVIa
cis ribbon_2_7 turnVIb
invaturn

Create Complex Expressions
13.3 Create Complex Expressions

Objects (atoms, bonds, etc.) can be combined, using standard operations, to
yield complex expressions.
When SYBYL operation prompts you for an object (atom, bond, etc.), you can
use any of the methods described in the previous section, which yields
exactly one object when interpreted. When you are prompted for an object
expression, you may enter a group of objects. Object expressions allow you to
combine various objects to produce a resultant set, which is the exact portion of
the molecule that you want to manipulate.
• Formats for Specifying Objects on page 202
13.3.1 Logical Operators

Expressions can consist of the logical operators union, intersection, difference,
and negation (represented by the symbols + or comma, &, - and ~, respectively)
and the elements to which they are applied.
In the discussions which follow, an abstract definition of a logical operation is

given using A, B, and C as general object sets and D as the general resultant set.
The general form of the allowable expression is very similar to the algebraic
form of mathematical equations. Parentheses group the elements of the
expression for evaluation in a specified order.
The Venn diagrams below illustrate the logical operators. Shaded areas
represent the selected set D which results from the indicated operations. The
outer circle represents the total set from which the subsets are chosen.
Union Intersection Difference Negation

In either set In both sets In first set and Do not have speci-
not in second fied property
D=A+B or D=A&B D=A-B D=~A
D=A,B

Note: Since SYBYL uses spaces as delimitors between commands and

arguments, spaces are not allowed in expressions.
Examples
Union
Locate all carbons and oxygens in a molecule and color them green.
COLOR ATOM <C>+<O> GREEN
Color all alpha carbons, other carbons, nitrogens, and oxygens red (these atoms
make up a peptide backbone).
COLOR ATOM CA,C,N,O RED
Intersection
Identify atoms in the active site of an enzyme and also in a helical secondary
structure:
LIST ATOMS {HELIX*}&{ACTIVE_SITE} BRIEF
This presumes that the sets {HELIX} and {ACTIVE_SITE} have been defined
previously.
Locate all carbons which have a partial charge between 0.0 and 0.10 in a
particular molecule and color them red.
COLOR ATOM <C>&{CHARGE(0.0,0.1)} RED
This example makes use of one of the built-in sets: {CHARGE}.
Difference
Color all atoms not in the backbone of a biopolymer yellow:
COLOR ATOM *-{BACKBONE} YELLOW
The asterisk selects all atoms and then the backbone atoms are subtracted.
{BACKBONE} is a built-in set defined for all polymers.
List all carbons not sp3 hybridized:

LIST ATOMS <C>-<C.3> BRIEF
Negation
Select sidechain atoms for a biopolymer, exclude backbone atoms:
COLOR ATOM ~{BACKBONE} YELLOW
This is functionally identical to the color command shown as the difference

operator example.

13.3.2 Parentheses and Grouping of Operations

When grouping operations into more complex expressions, keep in mind that
intersection has a higher precedence than union, just as multiplication has
precedence over addition in algebra. Parentheses are used to force evaluation of
the expression in a particular order by grouping objects and operators.
Examples
Display only heteroatoms in a molecule, combine a union operation with a

negation operation:
DISPLAY ~(<C>,<H>)
Locate all carbons and oxygens which are in hydrophobic residues of a protein:
DISPLAY (<C>+<O>)&{HYDROPHOBIC}
The set {HYDROPHOBIC} must have been defined previously.

Chapter 14.
Sets in SYBYL
A Set is a named collection objects: atoms, bonds, or substructures. Examples in

the context of a biopolymer are sidechain atoms, backbone bonds, co-crystal-
lized water molecules, active site. A set can be used as a shorthand notation for
groups of atoms, bonds, or substructures which are referenced often.
Some sets are closely associated with the particular molecules for which they
are defined (local sets), while others may be applied in a blanket fashion to any
molecule (global sets). Once applied to a particular molecule, the definitions of
all sets are stored in the molecular description along with the coordinates and all
other molecular data.
When you reference a set name in the context of an operation, the members of
the defined set are automatically identified as the object of the action. If the
request is for atoms or bonds, the specified substructures are expanded to their
respective atom or bond constituents automatically.
The diagram below shows sets used in SYBYL and their interrelationships.
• Global Sets on page 217—Set whose definition is applicable on a

system-wide basis, i.e., it may be applied to any molecule. of special
interest are the Global Sets in the Biopolymer Dictionary on page 218.
• Local Sets on page 220—Created for specification of objects in a
particular molecule. Membership is associated only with that molecule.
• Dynamic Sets on page 222—Uses a rule to define membership.
Membership is determined when it is referenced, by interpreting the
expression in the context of the current molecular description. Both local
and global sets can exhibit dynamic properties.
• Built-in Sets on page 223—Always a dynamic global set and based on
properties or geometrical relationships which are subject to change. Can
be applied to atoms, bonds, or substructures.

Chapter 14. Sets in SYBYL
• Static Sets on page 228—Membership is identified at the time of set

definition.
• Aggregates—Local sets, always static, and user-defined. If defined by a
dynamic rule, it is immediately evaluated and membership becomes
static. Aggregates are recognized by the minimizer as groups of atoms
and bonds whose relative geometry is not to be optimized. (See the
discussion of Aggregates in the Force Field Manual for additional infor-
mation.)
• User-Defined Sets—Either dynamic (local or global) or static sets
created by the user. Global sets defined by the user are always dynamic
and are used exactly as those carried in the macromol dictionary. In
some cases, a set can be defined equally well as static or dynamic,
depending upon whether membership is likely to change during the
course of the project. For example:
• Alpha_helical region of a peptide.
• Chair and boat conformations of six-membered rings in a polycyclic
structure.
• Charge range for atoms carrying an electrostatic charge between the
values of 0.1 and 0.5 esu.
• Working with Sets on page 229
• How to Use the Atom Expression Dialog on page 75 for examples of
how to use defined sets
• Definitions of SYBYL Objects on page 198

Global Sets
14.1 Global Sets

Global sets are dynamic sets not directly associated with any specific molecule.
They may be defined at any time and can be applied to any molecule. They are
always of the dynamic type. By their very nature they cannot include specific
objects. Once applied to a particular molecule, they are copied to that
molecule’s set list and remain associated with it, unless explicitly deleted. For
example, the definition of POSITIVELY_CHARGED.
Global sets which are built into the program are typically defined in the
macromol dictionary. When the dictionary is opened, sets are available for use
automatically.
14.1.1 Define a Global Set

DEFINE GLOBAL_SET object_type object_expr name comment
object_type Class of object to be members of set: ATOM, BOND or SUB-

STRUCTURE.
object_expr Set of objects of indicated class (evaluated only when set is
referenced).
name Name for set. Must be unique. First character must be alpha-
betic and a maximum of 30 additional characters must be
alphanumeric or underscores (_).
comment Arbitrary string associated with set.
14.1.2 Modify a Global Set

Create/Modify MODIFY GLOBAL_SET COMMENT set_expr {comment}
Comment via • set_expr—Expression indicating set to modify.
quotes when entering spaces or special characters.

Global Sets
Change Defini- MODIFY GLOBAL_SET DEFINITION set_expr

tion via Com- {object_exp}
mand Line: • set_expr—Expression indicating set to modify.
• object_expr—Rule for determining membership of the
dynamic set.
Global sets must be dynamic, hence the definition must be
in terms of a general expression rather than specific mem-
bers. The class of objects selected by a global set cannot
be altered by this procedure, only the definition.
Note: If a global definition is modified, it is modified in all instances associated

with the molecules in memory. If the local (molecule-associated) copy is
modified, it is no longer considered related to the global definition from which
it was derived. In that case, modification of the global set of the same name
does not affect the local copy.
14.1.3 Delete a Global Set

REMOVE GLOBAL_SET set_expr
set_expr Expression indicating set to remove, may include the wild-

card character (*). For example, to remove both g1 and g2,
enter g* or the expression g1,g2.
Note: If a global definition is deleted, its copies associated with the molecules
in the work areas are also deleted. If the local (molecule-associated) copy is
modified, it is no longer considered related to the global definition from which
it was derived. In that case, deletion of the global set of the same name does not
affect the local copy.
14.1.4 Global Sets in the Biopolymer Dictionary

Although you can define a new global set as it becomes necessary, several
global sets are already associated with the macromol dictionary and automati-
cally become available for use when the dictionary is opened.
The table below provides a complete listing of global sets currently available in
the macromol dictionary, accompanied by objects to which they apply and a
defining expression explaining how the various sets were created.
Name Objects Defining Expression
ACIDIC Substs {MONTYPE(asp,glu,tyr)}

BASIC Substs {MONTYPE(his,arg,lys)}

Global Sets
Name Objects Defining Expression
BLOCK Substs {MON-

TYPE(ace,nme,pyr,amd,for,nmt,nmm,cme,mes
,ees,boc)}
BULKY Substs {MONPROP(MOL_WT,140,9999)}
CALPHA Atoms CA
CAP Substs {MONTYPE(amn,cxl,ami,cxc)} for proteins
{MONTYPE(hb,he)} for DNA and RNA
DISULFIDE Bonds sg-cb-hg-lpg1-lpg2,sd-cg-hd-1pd1-1pd2
DNA Substs {MONTYPE(dA,dG,dC,dT)}
HYDROPHOBIC Substs {MONTYPE(gly,ala,ile,leu,met,phe,pro,
trp,val)}
MOD_AA Substs {MONTYPE(abu,aib,arz,asz,bal,cym,cyx,glz,
hcx,hcy,hid,hie,hip, hpr,hse,hyp,lyz,nle,nva,
orn,orz,phg,pse,psm,psz,ptm,pty,ptz)}
NEUTRAL Substs {MONTYPE(tyr,his,asn,cys,gln,ser,thr)} +
{HYDROPHOBIC}
POLAR Substs {MONTYPE(asp,glu,tyr,asn,gln,thr,ser,cys,
his,lys,arg)}
PURINE Substs {MONTYPE(dG,dA,rG,rA)}
PYRIMIDINE Substs {MONTYPE(dC,dT)} for DNA
{MONTYPE(rC,rU)} for RNA
RNA Substs {MONTYPE(rA,rG,rC,rU)}
STD_AA Substs {MONTYP(ala,arg,asp,asn,cys,glu,gln,gly,his,
ile,leu,lys,met,phe,pro,ser,thr,trp,tyr,val)}
SUGAR Substs {MONTYPE(glb,mab,maa,gaa,gab,frb,fra,dra,
drb,rba,rbb)}
Note: Atomic weights correlate with the latest accepted figures from IUPAC
and NIST. The average difference is 0.01% of the old values. In the cases of
unstable atoms, the values for the most stable isotope are used.
• IUPAC: Pure Appl. Chem. 2003, 75, 1107-1122
• National Institutes of Standards and Technology (NIST)
• Dictionary Files description in the Biopolymer Manual.

Local Sets
14.2 Local Sets

A local set consists of objects in a particular molecule. Membership is
associated only with that molecule. Local sets may be defined by any user at
any time. Examples are the definition of a protein’s active site and aggregates
used during minimization.
Local sets may be dynamic or static.

• Dynamic Sets on page 222
• Static Sets on page 228
When an atom or a bond involved in a local set is removed from the molecule,
the set membership is automatically updated.
14.2.1 Modify a Local Set
Menubar: Edit > Sets > Modify Set

Create/Modify MODIFY LOCAL_SET COMMENT set_expr {comment}
Comment via • set_expr—Expression indicating set to modify.
quotes when entering spaces or special characters.
Change Defini- MODIFY LOCAL_SET DEFINITION set_expr
tion via Com- {object_expr [merge]}
mand Line: • set_expr—Expression indicating set to modify.
• object_expr—Membership (for a static set) or rule for
determining membership (for a dynamic set).
• merge—NO/YES, for static sets only, whether to add to
or replace current definition.
For dynamic sets, there is no merge option; they are com-
pletely redefined by this command.
Change Name via MODIFY LOCAL_SET NAME set_expr {name}
Command Line: • set_expr—Expression indicating set to modify.
• name—Name for set.
First character of set name must be alphabetic and may be
followed by up to 30 additional characters, including
alphabetic, numeric, and the underscore (_). Names must
be unique among all other (GLOBAL or LOCAL) sets and
also among substructures.

Local Sets
14.2.2 Delete a Local Set

Delete a user-defined local set, static or dynamic, from a molecule’s
description.
Menubar: Edit > Sets > Delete Set

Command REMOVE LOCAL_SET set_expr
Line: • set_expr—Expression indicating the set(s) to remove,
may include wildcard character (*). For example, to
remove both s1 and s2, enter s* or the expression s1,s2.

Dynamic Sets
14.3 Dynamic Sets

A dynamic set is a group of objects whose membership is evaluated dynami-
cally (only when the set name is used in a command or is referenced by an
application routine). A standard object expression is analyzed at the time of
reference to determine the current set of objects meeting the requirements of the
expression. The expression must be valid for the type of object the set is to
contain.
Because objects are not permanently assigned to a set of this type, dynamic sets
are most often used to monitor properties of molecules which are subject to
change, such as conformation, charge, strain energy among many others.
14.3.1 Define a Dynamic Set
Menubar: Edit > Sets > Create Dynamic Set

Command DEFINE DYNAMIC_SET object_type object_expr
Line: name comment
• object_type—Class of object to be members of the set:
ATOM, BOND or SUBSTRUCTURE.
• object_expr—Expression of objects, of indicated class, to
include in set (evaluated only when set is referenced).
• name—Unique name for set. First character must be
alphabetic with a maximum of 30 more characters (alpha-
numeric or underscores (_)).
• comment—Comment string.
14.3.2 Examples of Dynamic Sets

Define all substructures (monomers) within 10 Å of atom C1 in residue A17 as
members of the set called ACTIVE_SITE:
DEFINE DYNAMIC_SET SUBSTRUCTURE {SPHERE(A17.C1,10)} \
active_site “10Å radius around A17”
If the atoms are manipulated (e.g., conformations are modified), membership in
this set can change.
Color the atoms that are members of the dynamic set ACTIVE_SITE:
COLOR ATOM {active-site} MAGENTA
The membership is evaluated at the time of reference according to the definition
rule. Substructures belonging to the set are expanded into their constituent
atoms for the execution of the command.

Built-in Sets
14.4 Built-in Sets

The membership of a built-in set is determined at the time it is referenced.
Built-in sets may not be created, removed, or altered by the user.
Built-in sets differ from the general dynamic set types:

• Evaluation rules are built into the program.
• They may require one or more arguments to direct their evaluation.
Required arguments are specified in parentheses after the set name,
separated with commas. For example, {SPHERE(C2,5)} specifies all
atoms within 5 Å of atom C2.
The table below contains a complete listing of built-in sets currently available in
SYBYL, the forms in which they are invoked (commands and arguments
required, if any), explanations, and examples.
AROMATIC {AROMATIC(atom_expr)}
• Atoms Atoms in the same aromatic system as the specified
atom(s).
LIST ATOM {AROMATIC(9)} BRIEF
BACKBONE {BACKBONE}
• Atom Set Atoms belonging to the backbone as defined in the
macromol dictionary.
COLOR ATOM {BACKBONE} RED
• Bonds {BACKBONE}
Bonds belonging to the backbone as defined in the mac-
romol dictionary.
SCAN {BACKBONE}
BIOPOLYMER {BIOPOLYMER(option1,option2,…)}
• Substructure Substructures in a biopolymer. Options are:
• PROTEIN—Selects amino acids in protein chains
(including modified amino acids). It is similar to
{SEQUENCE(*)}
• DNA—Selects nucleic acids in DNA chains.
• RNA—Selects nucleic acids in RNA chains.
• COFACTOR—Selects cofactor substructures, as
defined in the biopolymer dictionaries.
• WATER—Selects water substructures, as defined in
the biopolymer dictionaries.
• LIGAND—Selects substructures not included in the
above categories and not a carbohydrate, as defined
in the biopolymer dictionaries.
COLOR SUBSTRUCTURE {BIOPOLYMER(LIGAND)}
CYAN

Built-in Sets
BUMPS {BUMPS(atom1,atom2)}
• Atoms Atoms in one group having van der Waals contacts with
atoms of the other group. van der Waals parameters
stored in the file $TA_ASCTABLES/ATOM_DEF are
used.
Use TAILOR SET GENERAL
BUMPS_CONTACT_DISTANCE to define the cutoff dis-
tance. Negative values allow overlap of van der Waals
spheres, positive values prohibit it. Default is 0.0 Å.
COLOR ATOM {BUMPS(atom1,atom2)} MAGENTA
CHARGE {CHARGE(minimum,maximum)}
• Atoms Atoms having a residual charge in the specified range.
COLOR ATOM {CHARGE(-.05,-.01)} BLUE
CHIRAL {CHIRAL(atom_expr,RS)}
• Atoms Atoms of the specified chirality or pro-chirality. Spec-
ify the atoms to search as an expression. Chirality is
indicated by the second argument as: R, S, RS, PRO_R,
PRO_S, or PRO_RS. If RS or PRO_RS is entered, all cen-
ters are included in the set. The default is to search all
atoms (*) for all chiral centers (RS).
COLOR ATOM {CHIRAL(CA,S)} YELLOW
FINDCONF {FINDCONF(state1+state2+,sequence)}
• Substructures Monomers having the specified conformational state(s)
as defined in the macromol dictionary. Entering a
sequence limits the search to the specified regions of
the biopolymer (“*” searches whole biopolymer). Sepa-
rate conformational states by plus signs.
LABEL SUBSTRUCTURE {FIND-
CONF(ALPHA_HELIX,*)}
H_CONN_VIS_HEV {H_CONN_VIS_HEV(atom_expr,type)}
Hydrogen atoms that are connected to visible heavy
atoms. Valid types include: ALL, HBOND, NONHBOND,
POLAR, or NONPOLAR. It is used to display hydrogens
the Protein Viewer and in the Molecule Display Options
tool.
HBOND {HBOND(atom_expr,type)}
• Atoms Atoms of the specified type participating in hydrogen
bonds. Valid types include: ALL, DONOR, ACCEPTOR, or
HYDROGEN. Definitions for the donor and acceptor
atoms are in the parameter table $TA_ASCTABLES/
ATOM_DEF as H_ACCEPTOR and H_DONOR fields.
LIST ATOM {HBOND(1+2+3+4+5+6,donor)}
BRIEF

Built-in Sets
METAL {METAL}
• Atoms Atoms with a metallic ordinal number (according to the
periodic table). This set also includes metal atoms in
cofactors.
COLOR ATOM {METAL} PURPLE
MONPROP {MONPROP(keyword,minimum,maximum)}
• Substructures Monomers having the specified property as identified
by a keyword and (optional) minimum and maximum
values. Enter only the keyword to select all monomers
having that keyword. Enter the keyword and a mini-
mum to select monomers with the keyword whose
value matches the minimum. The keyword may be any
arbitrary string. Values may be real, integer, or string.
Properties are stored in the macromol dictionary
(molecular weight is stored as MOL_WT).
LABEL SUBSTRUCTURE {MON-
PROP(MOL_WT,150,200)}
MONTYPE {MONTYPE(type1,type2,...)}
• Substructures Monomers of the specified type(s). Types are defined
in the macromol dictionary. As many types as desired
may be specified as arguments. An asterisk (*) speci-
fies all substructures that are monomers.
LABEL SUBSTRUCTURE {MONTYPE(A,T)}
POSSIBLE_HBOND {POSSIBLE_HBOND(atom_expr,type)}
• Atoms Atoms of the specified type which can potentially par-
ticipate in hydrogen bonds. Valid types include:
• ALL
• DONOR—Potential H bond donor atom, attached to a
hydrogen or has at least one free valence.
• ACCEPTOR—Potential H bond acceptor.
• HYDROGEN—Hydrogen attached to an H bond
donor.
LIST ATOM {POSSIBLE_HBOND(*,all)} BRIEF
RINGS {RINGS(atom_expr,type)}
• Atoms Specified atoms which are included in rings of the
specified type. Types include:
• I—Internal rings (completely contained within a
substructure).
• E—External rings (crossing substructure bound-
aries).
• EI (IE)—Either internal or external.
If no arguments are entered, defaults to
{rings(*,EI)}.
COLOR ATOM {RINGS(*,E)} BLUE

Built-in Sets
• Bonds {RINGS(bond_expr,type)}
Specified bonds which are included in rings of the
specified type. Types include:
• I—Internal rings (completely contained within a
substructure)
• E—External rings (crossing substructure bound-
aries)
• EI (IE)—Either internal or external.
If no arguments are entered, defaults to
{rings(*,EI)}.
COLOR BOND {RINGS(*,I)} RED
• Substructures {RINGS(substructure_expr,type)}
Substructures in the expression, which are included in
rings of the specified type.
COLOR SUBSTRUCTURE {RINGS(*,E)} YELLOW
SEQUENCE {SEQUENCE(sequence1,sequence2,)}
• Atoms Atoms in monomers of the specified sequence(s).
Monomers are defined in the macromol dictionary. See
Specific Monomer Sequences on page 208 for more
information.
COLOR ATOM {SEQUENCE(GLY=PRO,GLY=GLY)}
BLUE
COLOR ATOM {SEQUENCE(A/1:25)} RED
COLOR ATOM {SEQUENCE(<,>)} MAGENTA
• Bonds {SEQUENCE(sequence1,sequence2,)}
Bonds in monomers of the specified sequence(s).
Monomers are defined in the macromol dictionary.
SCAN {SEQUENCE(GLY=PRO)}
• Substructures {SEQUENCE(sequence1,sequence2,)}
Monomers in the specified sequence(s). Monomers are
defined in the macromol dictionary.
LABEL SUBSTRUCTURE
{SEQUENCE(A=T=C,T=*=U)}
SIDECHAIN {SIDECHAIN}
• Atoms Atoms belonging to sidechains as defined in the macro-
mol dictionary.
COLOR ATOM {SIDECHAIN} RED
• Bonds {SIDECHAIN}
Bonds belonging to sidechains as defined in the macro-
mol dictionary.
SCAN {SIDECHAIN}

Built-in Sets
SPHERE {SPHERE(atom_expr,radius)}
• Atoms Atoms falling within sphere(s) of the specified radius.
The expression defines the sphere center(s). When mul-
tiple atoms are selected, the final set is the union of sets
of atoms within spheres of indicated radius about each
center. All spheres have the same radius.
COLOR ATOM {SPHERE(ALA23.CA,10)} MAGENTA
• Bonds {SPHERE(atom_expr,radius)}
Bonds falling within sphere(s) of the specified radius.
The expression defines the sphere center(s). When mul-
tiple atoms are selected, the final set is the union of sets
of bonds within spheres of indicated radius about each
center. Note: Only bonds with both endpoint atoms in
the sphere are accepted. All spheres have the same
radius.
SCAN {SPHERE(N15,8)}
• Substructures {SPHERE(atom_expr,radius)}
Substructures falling within sphere(s) of the specified
radius. The expression defines the sphere center(s).
When multiple atoms are selected, the final set is the
union of sets of substructures within spheres of indi-
cated radius about each center. Note: Substructure is
accepted, even if only one of its atoms falls within the
sphere. All spheres have the same radius.
LABEL SUBSTRUCTURE {SPHERE(G16,12)}
SUBST_SPHERE {SUBST_SPHERE(atom_expr,radius)}
Atoms, bonds, or substructures falling within sphere(s)
of the specified radius. The expression defines the
sphere center(s). When multiple atoms are selected, the
final SUBST_SPHERE set is the union of sets of sub-
structures included in spheres of indicated radius about
each center. Note: Substructure is accepted, even if
only one of its atoms falls within the sphere (identical
to sphere for substructures).
TO_ATOMS {TO_ATOMS(atom_expr)}
• Bonds Bonds with one or both atoms in the specified expres-
sion.
SCAN {TO_ATOMS(CA)} CYAN
• SYBYL Atom Types in the Force Field Manual.
• Global Sets in the Biopolymer Dictionary on page 218

Static Sets
14.5 Static Sets

Membership of a static set is determined by a standard object expression
analyzed at the time of definition. Once specified, this membership does not
change unless one of the elements is deleted from the molecule. In this case, it
is automatically removed from the set as well and the membership is redefined.
With the exception of set members deleted from the molecule, every time you
reference a static set, the same elements are selected. Only local sets can have
static properties.
The latitude with which you can define members of a static set provides great
flexibility in the manipulation of molecular data. For example, static sets can
define:
• Active site portion of an enzyme (select atoms or monomers involved)
• Diene and dienophile portions of a molecule designed to undergo an
intramolecular cyclo-addition reaction
• Glycone and aglycone portions of a nucleoside
• Acyclic precursor region of what becomes part of a larger structure upon
cyclization
In addition, in SYBYL’s Biopolymer program, static sets are automatically

generated when molecules are read in from Protein Data Bank files.
14.5.1 Define a Static Set
Menubar: Edit > Sets > Create Static Set

Command Line: DEFINE STATIC_SET object_type object_expr
name comment
• object_type—Class of object to be members of set:
ATOM, BOND or SUBSTRUCTURE.
• object_expr—Expression of objects, of indicated class,
to include in set. object_expr is not retained with set
definition.
• name—Unique name for set. First character must be
alphabetic with a maximum of 30 additional characters
(alphanumeric or underscores (_)). Default is the
current name plus and underscore and number.
• comment—Comment string. If you modify the set, the
default comment is the current comment plus _new.

Working with Sets
14.6 Working with Sets

When you modify, list, or remove sets, SYBYL displays a dialog containing the
defined sets. Click the molecule in the list and use the selection tools to specify
the desired sets to modify, list, or remove. Highlighting a set in the list also
highlights the atoms in that set in the SYBYL window.
The examples below show the dialogs invoked for a protein.
Options > List > Sets Options > List > Global Sets
Select a molecule: Select the molecule area and molecule from the list.
Buttons to assist in the selection of sets: select all, invert
selection, clear selection.

Chapter 15.
Libraries of Chemical Groups and Fragments
SYBYL provides functional groups and fragments that allow you to easily build
most molecules. In some instances, however, you may need to have additional
fragments included in the standard library. These operations can be accom-
plished once you know a little about the SYBYL file structure.
In this section, you will find:

• Group Library Structure and Contents on page 232
• Fragment Library Structure and Contents on page 233
• Using the Fragment Library: Load Fragments on page 109

Chapter 15. Libraries of Chemical Groups and Fragments
Group Library Structure and Contents
15.1 Group Library Structure and Contents

As supplied by Tripos, the group library contains a variety of small functional
groups frequently used in the construction of molecules. Each functional group
is represented as a distinct molecule within a SYBYL database:
ALLYL AMIDE BENZYL

CN CO CO2
CO2MINUS CS CYCLOHEXYL
EPOXY ETHYL ISOPROPYL
N-AMIDE N-BUTYL N-N
N-PROPYL N3 N=N
NH2 NO NO2
OCO OH ONO
OO PHENYL SEC-BUTYL
SH SO SO2
SO2N SO2O T-BUTYL
VINYL
For convenience, the molecules in the library are given these same names.
Each group has a unique attachment point, internally equal to the root atom of
the root substructure of the molecule. Externally, a convention has been estab-
lished which identifies the attachment point as the first atom in the molecule
name (except for Phenyl). The internal convention must be observed for all
user-added groups in order for commands like ADD GROUP to function properly.
• Chemical Group on page 128 for how to add functional groups to struc-
tures

Fragment Library Structure and Contents
15.2 Fragment Library Structure and Contents

As supplied by Tripos, the fragment library contains approximately 200 small
molecules (fragments) which can be used to build organic molecules with good
initial geometries. Each fragment is the result of averaged crystallographic
observations (i.e., averaged geometries from the Cambridge data file).
The library is organized in a hierarchical fashion, using both “sets” and

“classes”. If you are unfamiliar with this terminology, read about database
grouping mechanisms in Organize Molecules into Groups (Sets and Classes) on
page 175.
The basic idea is that each molecule in the fragment library is a member of one
(or more) static database sets. These sets form the lowest level of the hierarchy,
and group together those molecules which are very closely related in structure
and/or function. At higher levels of the hierarchy, those molecules related in a
more general sense appear in the same group. This produces a structure which
looks like an inverted tree, with general categories at the top diverging into
more and more specific categories until, at the bottom, a single molecule is left.
For example, one of the high-level categories is “Cyclic Systems”—clearly a

very general grouping. From this category you may descend to heterocyclic
systems with two rings, then to those with one heteroatom, then to 56 ring
systems. At this point you reach the lowest level categories, those consisting of
static sets of actual molecules where, in this case, you would find indole or
benzofuran.
Access:
• File > Get Fragment
• FRAGMENT
• See Load Fragments on page 109.

The lowest level groups—those which contain the actual molecules—are static
sets, while all higher level categories are dynamic classes, defined as the union
of those groups directly under them. Thus the “56 Systems” are contained in a
static set, such as FIVESIX, but the group which corresponds to “1 Heteroatom”
in the above diagram is a dynamic class defined as the union of FIVESIX and
SIXSIX (FIVESIX+SIXSIX). Similarly, “Heterocyclic 2 Rings” is a dynamic
class defined as the union of “1 Heteroatom”, “2 Heteroatoms” and “>2
Heteroatoms”.
Tripos’ standard fragment library contains about 200 molecules partitioned into
44 static sets, and categorized into a hierarchy comprised of 17 dynamic classes.
Below is the full listing of sets and classes provided by Tripos to organize the
fragment library. In the listing, the dynamic classes are represented in italic
script, all others are static sets.

A: Acyclic Functions
• AA: Carbon Only
• AB: Function N
• AC: Function O
• AD: Function S
• AE: Function NO
• AF: Function SO
• AG: Function PO
• AH: Other
B: Cyclic Functions
• BA: Homocyclic, 1 Ring
BAA: Saturated
BAB: Unsaturated, 1 Double Bond
BAC: Unsaturated, 2 Double Bonds
BAD: Unsaturated, >2 Double Bonds
BAE: Aromatic
• BB: Homocyclic, 2 Rings
BBA: Saturated
BBB: Unsaturated
• BC: Homocyclic, 3 Rings
• BD: Homocyclic, 4 Rings
BDA: Steroids
BDB: Other
• BE: Heterocyclic, 1 Ring
BEA: 1 Heteroatom
• BEAA: 5 Membered Ring, Saturated
• BEAB: 5 Membered Ring, Unsaturated
• BEAC: 6 Membered Ring, Saturated
• BEAD: 6 Membered Ring, Unsaturated
• BEAE: Other
BEB: 2 Heteroatoms
• BEBA: 5 Membered Ring, Saturated
• BEBB: 5 Membered Ring, Unsaturated
• BEBC: 6 Membered Ring, Saturated
• BEBD: 6 Membered Ring, Unsaturated
BEC: >2 Heteroatoms

• BF: Heterocyclic, 2 Rings

BFA: 1 Heteroatom
• BFAA: 56 Systems
• BFAB: 66 Systems
BFB: 2 Heteroatoms
• BFBA: 56 Systems
• BFBB: 66 Systems
BFC: >2 Heteroatoms
• BG: Heterocyclic, 3 Rings
BGA: 1 Heteroatom
• BGAA: 656 Systems
• BGAB: 666 Systems
• BGAC: 676 Systems
BGB: 2 Heteroatoms
• BGBA: 666 Systems
• BGBB: 676 Systems
BGC: >2 Heteroatoms
C: Amino Acids
D: Nucleic Acids
• DA: Bases
• DB: Ribose Monophosphate
E: Biologically Important Molecules
• EA: Vitamins
• EB: Sugars
• EC: Lipids

Chapter 16.
Advanced SYBYL Features
As you gain familiarity with SYBYL you may want to explore the following
features:
• Automatic Command Execution at SYBYL Startup on page 238
• Execute a SYBYL Command on Multiple Molecules on page 239
• Define Markush Atoms on page 241

Chapter 16. Advanced SYBYL Features
Automatic Command Execution at SYBYL Startup
16.1 Automatic Command Execution at SYBYL

Startup
You may customize the SYBYL interface for your own use by storing in a file
the SYBYL instructions to be executed every time you start a new session.
This file, called sybyl.ini, must be placed in your home directory ($HOME on
Linux or Documents and Settings on Windows).
This file can typically be used to load your preferred font type and size or to
specify the colors used when working with UNITY features.
For additional information turn to the Toolkit Manual:

• Customizing SYBYL
• A Sample sybyl.ini File

Execute a SYBYL Command on Multiple Molecules
16.2 Execute a SYBYL Command on Multiple

Molecules
Use Default Mole- ALLMOLS sybyl_command
cule Area: The command syntax must include a molecule area (as
a regular argument or as part of an atom or bond
expression). The default is M1. The ALLMOLS com-
mand applies the SYBYL command, substituting the
default area as needed, to every molecule area in turn.
If you do not know the entire command syntax, you are
prompted for information needed to complete the com-
mand.
Use Non-Default ALLMOLS BASE mol_area
Molecule Area: This command must precede the ALLMOLS command
line. It designates the molecule area to substitute in the
loop. You then must include that molecule area in the
ALLMOLS command.
Use Subset of Mol- ALLMOLS GROUP mol_area_expr
ecules: This command must precede the ALLMOLS command
line. It designates the set of molecules to which subse-
quent ALLMOLS commands will apply. Note: The opera-
tion will affect all molecules in the GROUP as well as
the BASE molecule, even if it is not specifically
included in the GROUP.
BASE and GROUP remain in effect until they are changed or until the end of the
session.
The operation you want to perform must be possible on all molecules, otherwise
an error message is issued for every failed attempt. For example, coloring all
alpha helices will fail on molecules that do not contain that secondary structure.
Examples:
The following examples assume four molecules in M1, M2, M3, M4, respec-
tively, all having backbone, heteroatoms, and hydrogen atoms.
Label all heteroatoms in all molecules on the screen. BASE and GROUP are
assumed to have their default values of M1 and *, respectively.
ALLMOLS LABEL HETERO M1(*)
Color backbones in the molecules in M1, M3, and M4 yellow. BASE is assumed
to have its default value of M1. (The molecule in M2 is unchanged.)
ALLMOLS GROUP M1,M3,M4
ALLMOLS COLOR ATOM M1({BACKBONE}) YELLOW

Execute a SYBYL Command on Multiple Molecules
Remove hydrogens from the molecules in M2, M3, and M4. (The molecule in
M1 is unchanged.)
ALLMOLS BASE M2
ALLMOLS GROUP M3,M4
ALLMOLS UNDISPLAY M2(<H>)

Define Markush Atoms
16.3 Define Markush Atoms

Markushes are lists of groups of atoms which can provide constrained
variability in a pattern or structure. For example, a markush atom that represents
all halogens would be:
Hal:F|CL|BR|I
When a SYBYL session is started predefined Markushes are loaded from

$TA_ROOT/tables/markush.defs. However, using the methods discussed
below, you can create your own set of Markush definitions, save them to a file,
and load them instead.
• Define a Markush on page 241
• Delete a Markush on page 242
• List Currently Defined Markushes on page 242
• Load Markush Definitions from a File on page 242
• Modify a Markush Definition on page 242
• Save a Markush Definitions to a File on page 242
16.3.1 Define a Markush

Note: A newly defined Markush is only available during the current SYBYL
session, unless it is saved to a file and then loaded.
Menubar: Applications > Library Design > Markush >

Define
Command Line: MARKUSH DEFINE name definition
• name—Name for new Markush atom.
• definition—SLN defining the Markush (refer
to the SLN Manual). To create an opaque
Markush (a Markush with an empty
definition), simply press the carriage return at
the prompt for the definition.

Define Markush Atoms
16.3.2 Delete a Markush

Delete
Command Line: MARKUSH DELETE name
16.3.3 List Currently Defined Markushes

List the contents of the file of Markushes that is currently loaded (by default
this is $TA_ROOT/tables/markush.defs). Any Markushes that have been
defined during the current SYBYL session are included in the list as well.

List
Command Line: MARKUSH LIST
16.3.4 Load Markush Definitions from a File

Load
Command Line: MARKUSH LOAD filename
16.3.5 Modify a Markush Definition

Any modifications to Markush definitions will not exist beyond the current
SYBYL session unless they are saved to a file.

Modify
Command Line: MARKUSH MODIFY name definition
• name—Name of Markush to modify.
• definition—New SLN defining the Markush.
16.3.6 Save a Markush Definitions to a File

For any user-defined Markushes to be available during subsequent SYBYL
sessions, they must be saved to a file and then loaded during that session.

Save
Command Line: MARKUSH SAVE filename

SYBYL Basics Index
A Attributes
remove
Abort from atom 121
a command 31 from bond 127
Access help 21 from stereo atom 132
from stereo bond 132
Acidic global se 218
Automatic command execution 238
Add
atom 118 Average molecule 136
bond 125
chain 119
features and constraints 145
B
group 128 Backbone
hydrogens 120 built-in set 223
pseudo-atoms 119 Basic global set 218
rawatom 118
Basics
Aggregate introduction 7
sets 216
Bibliography
ALLMOLS 239 chirality assignment 130
Alternate atom types 123 SHAKE algorithm 136
Amide bond 205 BIOPOLYMER
Amino acid sets 218
global sets 219 Biopolymer
Angle built-in set 223
between planes 150 Block
measure 148 global set 219
modify 127 Bond
Aromatic bond 205 add 125
Aromatic built-in set 223 angle list 149
attributes 130
Atom definition of types 71
add 118 expression rules 205
chirality attribute 130 length
expression rules 203 list 149
modify 122 naming conventions 205
naming conventions 203 remove 126
rawatom 118 remove attributes 127
remove 121 selecting 61
renumbering 144 stereo attributes 130
selecting 61 SYBYL object definition 198
SYBYL object definition 198 type
Atom expression modify 127
dialog 67 Bond expression
Atom types dialog 67
alternate set 123 Building
modify 123 small molecule 111
Atomic coordinate 223
Built-in sets
topography 149
Bulky global set 219
Attach
chain 119, 128 Bumps
SYBYL-X 1.1 SYBYL Basics Index-243

built-in set 224 Customize
start up 238
C
C-alpha carbon global set 219
D
Cap global set219 DATABASE 180
CAPTURE 194 Database
add molecules 174
Center of mass 138 classes 175
Centroid 139 close 168
Chain copy contents to new database 168
of atoms 119 copy database directories 181
create empty database 167
Change create table 172
molecule name 133, 176 DATABASE command list 180
substructure name 129 define alias 168
Charge define class or set 176
built-in set 224 example 160
modify 122 delete 175
CHIRAL 130 deleting database directories 181
get a molecule 169
Chiral built-in set 224 grouping mechanisms 175
Chirality list
atom attribute 130 contents of open database 173
check 101 molecule and group information 173
invert 131 open databases 173
Class open 167
define in a database 175 rename 176
reorganize contents 177
Clear the screen 89 save as 174
Collect commands into a file 191 save to Mol2 file 178
Command mode search 170
special characters 31 example 163
sets 175
Conformation show status 173
naming conventions 210 specify default database 168
SCAN 136 tutorial 159
valid state names 210 unlocking 166
Connectivity dbtranslate
quick bonds 125 dialog 44
Console 30 options dialog 46
Continuous Drawing Mode dbtranslate O/S utility
Cancel point of attachment 112 see UNITY manual
Conventions (see Names) use in MDL Mol conversion 43
Coordinates dbunlock O/S utility 166
list 149 Default molecule area 54
MODIFY 122 Defining
Copy 55 center of mass 139
molecule area contents 55 centroid 139
Creating dynamic set 222
small molecules 111 extension point 140
global set 217
Index-244 SYBYL Basics SYBYL-X 1.1

line 141 E
normal 142
plane 143 Edit
static set 228 text files 49
UNITY features 145 EDITOR 49
Delete Environment variable
atom attributes 121 EDITOR 49
atoms 121 SAVE_SESSION_DIR 184
bond attributes 127 TA_HIDE_UNLICENSED_PRODS 26
connected atoms 121
Evaluating
hydrogens 121
center of mass 139
Deleting centroid 139
all atom attributes 121 extension point 140
all bond attributes 127 line 141
atom 121 normal 142
bond 126 plane 143
center of mass 139
Extension point 140
centroid 139
extension point 140 External ring
global set 218 SYBYL object definition 200
line 141 Extract structures
local set 221 from molecule area 55
molecule in a database 175
non query atoms 145
normal 142 F
plane 143 Features
stereo atom attributes 132 center of mass 138
stereo bond attributes 132 centroid 139
substructure 129 extension point 140
SYBYL session 189 line 141
UNITY feature 146 normal 142
Difference plane 143
operator SYBYL object definition 199
in a database 171 UNITY 145
in object expressions 211 File formats
Directory .demo file 193
list database contents 173 convert between molecular formats 44
Display area 52 File selection dialog 34
diagram 53 Files
Distance convert between molecular formats 44
measure 148 edit 49
modify 127 reading/writing
219
Disulfide global set MDL Mol file 42
SD file 42
DNA global set 219 SLN 42
Double bond 205 Files created
Dummy atom 138, 139, 142, 143 CAPTURE 194
Dynamic set 222 COLLECT 191
(see also Local sets) DATABASE 167
SYBYL object definition 201 WRITE_FILE2 178
MDL Mol files 42

Mol2 39 with SYBYL 13
SD files 42 Internal ring
Fill valences 120 SYBYL object definition 200
Findconf built-in set 224 Intersection operator
FRAGMENT 109 in a database 171
in object expressions 211
Fragment
library 233 Invert chirality 131
structure and contents 233
Freeze J
coordinates before merging 56 Join
Fuse ring 134 groups or molecules 135
tutorial 103
Journal
COLLECT command 191
G PHOTO command 194
Geometry
measure 147 K
modify 127
Kollman atom types 123
Global
dictionary set 218
set 217 L
Grid Libraries 231
SKETCH 117 License requirements
Group library 232 SYBYL basics 8
add 128 Line 141
SKETCH 115
structure and contents 232 List
object information 155
Load molecule 16, 33
H commands 41
H_CONN_VIS_HEV built-in set 224 fragment library 16
Hardcopy 156 Local set 220
Hbond built-in set 224 Logical operators in object expressions
difference 211
Height measurement 148
grouping 213
Help 21 intersection 211
special characters 31 negation 211
Hide menu options 26 union 211
Hydrogens Lone pair
add 120 MODIFY 122
delete 121
Hydrophobic M
global set 219
Manage
SYBYL session 183
I MARK_RS isomerism 130
Information MARK_ZE isomerism 130
report on atom, bond, or substructure 154 Markush 241
Interacting

MDL Mol save 39
convert to molecular spreadsheet 43 save as 20
convert to UNITY hitlist 43 save in a database 174
MDL Mol file selecting 61
42
read/write files split 121
type 134
MDLMOL command 42 writing files 33, 34
Measure Molecule area
angle 148 default 54
distance 148 naming conventions 207
height 148 rules 52
plane angle 150 SYBYL object definition 198
torsion 148
UNITY features 151 Molecule expression
dialog 74
Menubar 26
shortcuts 27 Monomer
sequence expression rules 208
Merge 56 sequence naming conventions 208
atoms 56
exceptions 56 Monprop built-in set 225
merging features 56 Montype built-in set 225
non-unique atom 56, 58
non-unique atoms example 58
set 57 N
structures 56 Name
unique atom 56 atom 203
Metal built-in set 225 modify 122
bond 205
Modified amino acid global set 219
chain 209
Modify conformation specification 210
angle 127 general conventions 202
atom 122 local set 220
bond 127 molecule area 207
distance 127 molecules 207
global set 217 monomer sequence 208
local set 220 generic 208
molecule 133 specific 208
substructure 129 set 207
torsion 127 substructure 206
UNITY feature 146
Negation operator
Mol2 41 in a database 171
Molecular Spreadsheet in object expressions 211
MDL Mol file conversion 43 Neutral global set 219
Molecule New
build 95 SYBYL session 189
defining features 138
Non-bonded
deleting in a database 175
list 149
evaluating features 138
expression rules 207 Normal 142
extracting atoms 55 Notebook
modify 95, 133 COLLECT command 191
naming conventions 207 PHOTO command 194
reading files 33, 34

O Read molecule 33
fragment library 16
O/S utilities
Read/save database molecules 178
dbtranslate
see UNITY manuals Recording
use in MDL Mol conversion 43 COLLECT command 191
dbunlock 166 PHOTO command 194
Object Recover contents of molecule area 94
definitions 198 References
Open chirality assignment 130
saved SYBYL session 189 SHAKE algorithm 136
34
Open file dialog Reflect atoms 132
Open molecule file 33 Remove
all atom attribute 121
Operator
all bond attribute 127
difference 171, 211
atom 121
grouping 213
bond 126
intersection 171, 211
bond attributes 127
negation 171, 211
center of mass 139
precedence 171
centroid 139
union 171, 211
extension point 140
global set 218
P line 141
local set 221
Pause 193 non query atoms 145
Pen up 112 normal 142
PHOTO 191, 194 plane 143
stereo atom attribute 132
Plane 143 stereo bond attribute 132
measure angle 150 substructure 129
reflect through 132 UNITY feature 146
Play back session RENUMBER 144
COLLECT and TAKE files 191
command file 192 Replace chain 119, 128
Polar Reset the screen 89

global set 219 Restore
Possible_hbond built-in set 225 SYBYL session 189
Printing 156 Restore from stack

undo the last operation 94
PRO RS isomerism 130
Retrieve molecules 169
Purine global set 219
Ring
Pyrimidine global set 219 built-in set 225
fusion 134
Q list 155
ring fusion tutorial 103
Query expressions 170 SYBYL object definition 200
QUICKBOND command 125 RNA global set 219
Root atom 134
R Rotation
Rawatom, adding 118 of molecules 17

RS isomerism 130 keyboard 32
menubar 27
mouse 27
S
Sidechain
Save as 226
built-in set
molecules 39 Single bond 205
SAVE_SESSION_DIR 184 Sketcher 111
Saving add Z coordinate 114
molecule in a file 33 branching 113
formats 39 change atom types 112
molecules 39 check chirality 101
in a database 174 draw a ring 114
select molecule(s) 39 draw multiple bonds 113
sketch 102 move an atom 116
SYBYL session 184 save 102
Scanning techniques 111
torsions 136 toolbar items 115
tutorial 96
SD file
read/write files 42 SLN
read/write file 42
Search
database 170 SLN typer 123
Select objects 61 Small molecule building (see SKETCH) 111
Sequence Sphere built-in set 227
built-in set 226 Spiro fusion 135
Sequence expression Split molecule 121
dialog 67
Standard amino acids
SESSION 183 global set 219
Session 183 Starting
delete 189 SYBYL 13, 25
new 189
Static set 228
open saved session 189 define 228
restore 189
SYBYL object definition 201
save 184
Store molecules 174
Sets 215
aggregates 216 Subst_sphere built-in set 227
built-in 223 Substructure
database 175 expression rules 206
dynamic 222 modify 129
for biopolymers 218 naming conventions 206
global 217 remove 129
local 220 root 129
naming conventions 207 selecting 61
static 228 SYBYL object definition 198
SYBYL object definition 201 type 130
user-defined 216
Substructure expression
working with 229
dialog 67
SHAKED command 135 Sugar global set 219
Shortcuts
dialogs 27

T in a database 171
in object expression 211
TABLE
UNITY
DATABASE 172 defining features 145
TAKE 192 MDL Mol file conversion to hitlist 43
Tear-off menus 26 modify feature 146
remove
TMPDIR environment variable 177 features and constraints 146
To_atoms built-in set 227 non query atoms 145
Toolbar User-defined sets 216
overview29
Topography 149
Z
Torsion
list angle 149 ZAP 89
measure 148 ZE isomerism 130
modify 127
Translate
options 46
Translate molecular formats 44
Translation
of molecules 17
Triple bond 205
21
Tripos Bookshelf
TTY command 193
Tutorials
atom selection 75
bond selection 82
building a small molecule 96
file format 193
interacting with SYBYL 13
ring fusion 103
sketching a small molecule 96
small molecule sketching 96
substructure selection 85
U
UIMS2 variables
angle 148
collect file 192
database name 167, 168
distance 148
height 148
photo file 195
plane angle 150
torsion 148
Undo last action 94
Union
operator

Manual SyByL

Hochgeladen von

Dokumentinformationen

Copyright

Verfügbare Formate

Dieses Dokument teilen

Dokument teilen oder einbetten

Freigabeoptionen

Stufen Sie dieses Dokument als nützlich ein?

Sind diese Inhalte unangemessen?

Copyright:

Verfügbare Formate

Manual SyByL

Hochgeladen von

Copyright:

Verfügbare Formate

Basics Manual

1699 South Hanley Rd. Phone: +1.314.647.1099

SYBYL-X 1.1 SYBYL Basics TOC-3

TOC-4 SYBYL Basics SYBYL-X 1.1

SYBYL-X 1.1 SYBYL Basics TOC-5

Introduction to SYBYL Basics

SYBYL uses computer analysis to assist in the description and prediction of

When combined with SYBYL applications, SYBYL Base provides a completely

SYBYL-X 1.1 SYBYL Basics 7

1.1 License Requirements for SYBYL Basics

SYBYL-X introduced a simplified licensing scheme in which the “SYBYL”

Two additional keys perform the following functions:

Additionally, a “BioPolymer” license:

8 SYBYL Basics SYBYL-X 1.1

1.2 What is New with SYBYL Basics Features

New in SYBYL-X 1.1

Atom rendering is now part of the molecular description and

The SYBYL Window

SYBYL-X 1.1 SYBYL Basics 9

Expression Dialog Redesign

See the Expression dialog description for more information. [SYBYL-X]

New Look for the SYBYL Sketcher

The Sketcher operates on different molecule areas depending on atom selection:

10 SYBYL Basics SYBYL-X 1.1

Reading .sd Files

SYBYL-X 1.1 SYBYL Basics 11

Quick Introduction to SYBYL

Run this tutorial to learn some basics operations in SYBYL:

A Matter of Time: This tutorial requires about 5 minutes of personal time.

2.1 Start SYBYL

Start the SYBYL program using Trigo:

SYBYL-X 1.1 SYBYL Basics 13

Explore the SYBYL Window

When you initiate an operation by clicking a menu item, no other operation is

14 SYBYL Basics SYBYL-X 1.1

Note: The menubar and command line are available simultaneously.

SYBYL-X 1.1 SYBYL Basics 15

2.2 Load Molecules

2.2.1 Load a Molecule from a File:

¾ File > Import File ( )

¾ In the Open File dialog, click [$TA_DEMO] in the Bookmarks section

¾ Select example.mdb in the Directory Navigation list in the center.

¾ Select dicloxacillin.mol2 in the Selection list on the right then press

2.2.2 Load a Molecule from the Fragment Library:

¾ Select VITAMIN B2 in the list of available molecules and press OK.

2.2.3 Change the Display

¾ Click on the Display toolbar and select Half.

16 SYBYL Basics SYBYL-X 1.1

SYBYL displays the molecules in display areas D1 (right) and D2 (left).

2. Toggle the display for each molecule off and on.

¾ Click on the Molecule toolbar.

2.3 Rotate, Translate, and Scale Molecules

2.3.1 Move All Objects Together

Move All Objects Mouse Keyboard

Linux Usage Note

SYBYL-X 1.1 SYBYL Basics 17

• System (or Applications) > Preference > Windows

2. Rotate the molecules about the Z-axis.

2.3.2 Move Selected Objects Only

Move Selected Objects Mouse Keyboard

3. Move dicloxacillin to the upper right corner.

An alternative method is to change the mouse focus using a toolbar icon.

¾ Clear the selection first by clicking on the Selection toolbar.

18 SYBYL Basics SYBYL-X 1.1