You are on page 1of 44

Protein Data Bank Editor by JL Manual

By Jonas Lee University of California – Berkeley Department of Chemistry GNU General Public License Copyright© 2008


Author’s Note
PDB Editor by JL is the standalone Java Graphic User Interfaced application for the quick data manipulation and extraction of the Protein Data Bank files. I, who is trained as a protein crystallographer, was very dissatisfied with tools available to manipulate PDB files, which is often times very rare but also very unfortunate occasion. Conventional spreadsheet program can be setup easily to parse and coordinate contents, but the PDB’s column fixed data often does not allow you to easily save the data back to usable format. Several people have noted that you can use Perl and Awk, but I was more dissatisfied with writing scripts and debugging interpreter languages that doesn’t come with Integrated Development Environment in Linux command shells.

I have setup the program for quick manipulation and extraction. Knowing that the most manual PDB manipulation requires either repetitive or systematic inputting of values, the column are edited simultaneously as user selects multiple rows and type in their value or simple math formula they need. Data extraction is done much like in the spreadsheet, where you can easily extract data and bring in the data in tab delimited format by a clipboard commands. Several common functions I often use are implemented as well. Although they are very similar to PDBSET functions from CCP4, I changed them to do selective manipulation. It was my way of relieving stress from generating new PDB files everytime when you have to use command line based PDB manipulation tools.

This program is currently under development, and hopefully become the base platform for the quick visual manipulation.


Table of Contents
Author’s Note ------------------------------------------------------------------------------------------ 2 I. System Requirements, Installation, and Running the Program ------------------------------ 4 II. Main Window --------------------------------------------------------------------------------------6 Main Menu List --------------------------------------------------------------------------------------- 7 III. Coordinate Tab -----------------------------------------------------------------------------------10 Column Label Table -------------------------------------------------------------------------------- 11 Changing Displayed Columns --------------------------------------------------------------------- 12 Basic Coordinate Manipulation -------------------------------------------------------------------- 13 Advanced Coordiante Selection & Manipulation : “Search & Select” ----------------------- 15 Advanced Coordiante Selection & Manipulation : “Edit Atom” ----------------------------- 18 Coordinate Data Import & Export by Clipboard Action --------------------------------------- 20 Coordinate Data Import & Export in PDB Format by Clipboard Action -------------------- 21 IV. Title/Remark, Primary Structure, Secondary Structure Tab ------------------------------ 23 Data Export in Tab-Delimited Format by Clipboard Action ---------------------------------- 24 Data Import/Export in PDB Format Text by Clipboard Action ------------------------------- 25 V. Coordinate Tools -------------------------------------------------------------------------------- 26 Editing Spacegroup, unit cell, and SCALE matrix --------------------------------------------- 26 Residue Number and Chain ID Editor Tool ----------------------------------------------------- 28 Editing CONECT records --------------------------------------------------------------------------30 Generating Symmetry Mates and Exact One Fractional Coordinate Cell ------------------- 32 Rotate / Translate Selected Atoms ---------------------------------------------------------------- 34 Extracting Coordinate Statistics --------------------------------------------------------------------35 Extracting Protein Sequence from SEQRES or ATOM / HETATM ------------------------- 36 Tabulating closest atom distances around atoms or defined coordinates --------------------- 37 GNU Public License --------------------------------------------------------------------------------- 39


I. System Requirements, Installation &Running the Program
System requirements
Pentium III or above Operating System that supports Java SE 6 or above : • • Windows 2000 or above, Solaris, Linux (download from Mac OS X 10.5 (download patch from

50 Mbytes of free physical or virtual memory space 2 Mbytes of free disk space

* If you are running Mac OS X 10.4 or below, please urge Apple to make Java 6 update. They are being really lazy and malicious considering that Java 6 had been released almost two years ago, and looking at them selectively releasing path only on 10.5.

Installation & Running
No installation is necessary (I am still looking for a good multi-platform deployment software). Program can be run in the command shell by going to the directory containing downloaded jar file and typing java –jar PDB_Editor.jar OR java –jar PDB_Editor.jar <OPTIONAL PDB filename>

To spare you from the nightmare of typing the command every time you want to run a program, it will be good idea to make a shortcut. As most of you have already noticed by looking at <OPTIONAL PDB filename>, you can also link with PDB extensions for more quick access.


” before your shell name.jar file>’ 5) Now you can type in “pdbeditor <Filename>” in Terminal to run the editor.jar file. 5 . and click “Finish” 6) OPTIONAL : You can put it in the Start menu or Quicklaunch by dragging it into it. 2) Select “New” Æ “Shortcut” 3) Click “Browse”. “/bin/bash” in #1. <Your Shell Name> is anything that follows “/bin/” Therefore if you see. you are suppose to enter “gedit .<Your Shell Name>rc” There is a period “. Select PDB_Editor.bashrc” 4) Depends on the shell type one of the following at the very bottom of the page : • • Bash : alias pdbeditor = ‘java –jar <Full path of PDB_Editor. 5) Click “Next” Give appropriate name.Making shortcut in Windows 1) Right clicking on the desktop.jar file>” Tcsh & Csh : alias pdbeditor ‘java – har <Full path of PDB_Editor. and click “OK” 4) Follow the screenshot below by typing “javaw –jar” in front of the displayed filename. Making Permanent Alias in Linux 1) Find which shell you are using by opening Terminal and entering “echo $SHELL” 2) Go to your home directory by entering “cd ~” 3) Edit your shell configuration by entering “gedit .

Label key components in the main window . you will learn to . All the buttons in the toolbar has tooltip function. Main Window In this chapter. Nothing really interesting to discuss about.II. 6 . as well as. temporary function tip will be displayed in the statusbar when you place mouse over it.Give brief summary of each commands in the Main Menu It’s very common GUI window.

You can bring it by copying it and pasting back ƒ ƒ “Copy / Cut in PDB Format” is to put in clipboard in 80 column PDB line format that is used in the PDB file “Paste” command will recognize whether or not it’s tab delimited or PDB format – You can directly paste information from other PDB files by directly copy from the text editor.Main Menu List • File – Probably don’t need separate discussion about this if you can get the program to work • Edit – General manipulation and clipboard actions o Undo/Redo – Only works for atom manipulation now o Copy/Cut/Paste ƒ Just “Copy” stands for copy to clipboard in Tab delimited format – Good for carrying data to spreadsheet manipulation. Top/Bottom – Moves selected atoms in the direction you requested • Delete – Series of delete commands to trim your PDB coordinate o Delete Atom o Delete H atom / 0-occupancy / Alternate conformation o Delete Anisotropic temp factor / Sigma coordinate / Sigma temp factors o Be sure that there is a difference between “Selected Atoms” – only process selected rows VS. “All Atoms” – process all rows • Select – Ways to quickly search & select specific records 7 . o Open Edit Coordinates Window – Main coordinate manipulation window o Insert Empty Atoms – Inserts blank atom with all default value 0 or blank o Move Atom Records Up/Down.

o Search and Select Window – Main coordinate search window o Invert selections – Stop selecting rows that are currently selected. Good for frame shifting the residue numbers o Edit Atom Connectivity – Edit CONECT records o Reset Atom Numbers – Reset atom number starting from the first record as 1 and increment by sorting o Fix Elements from Atom Name – Fix element name for known residues – Had a problem with SHELX output when I was doing some PDB analysis o Correct Atom Ordering – It sorts atom by Chain ID > Residue Number > Atom name. and select all other rows that are not selected right now o Select all rows / columns – Extend current selection to requested direction o Select all atoms in Chain ID / Residue ID – Check all chain ID / residue ID in the current selection then search all atoms to extend selection match o Select All Protein / DNA / RNA / Solvent / Unrecognized atoms – Check all atoms using registered type residue name and select all match • Modify – Misc functions I wanted to have when I edited PDB file o Edit Space group info – Edit CRYST and SCALE parameters o Edit Residue Number & Chain ID – Serial residue number editor. undo/redoable operation so utilize it without hesitation • Calculate o Generate symmetry mates o Rotate and translate atoms 8 . Powered up from the last [LOVE?] rejection – now try to correct ordering of residues with insertion codes by searching for closest Nterm and C-term connections o Quick sort / Sort by multiple criteria in the quick sort – As name implies.

residues in linear fashion for sequence with complicated insertion code ordering o Find closest atom distances – Find closest atom from selected point. Also undo/redoable action. as well as. or residues. • Option – Mostly disabled debugging functions. Good for tabulating closest atom distances around the ligand o Reduce to Ca / Poly Ala – Always handy to have when generating figures and MR. Again powered up from the last [LOVE?] rejection – Now you can extract from SEQRES records. as well as.o Calculate number statistics – Calculate average / standard deviation / maximum / minimum for all atoms in the coordinate. selected row of atoms o Extract sequence– Extract recognized residues in linear single letter or three letter code form. atoms. Nothing really interesting except changing column displayed 9 .

How atom data is manipulated by mouse & keyboard .III.How to effectively manipulate atoms using “Search and Select” and “Edit Atom” window . and how to change columns displayed .How clipboard actions can be manipulated to import/export PDB formatted texts TIP : Full data type name will be displayed by tooltip if you hover mouse over the table header 10 . you will learn to .Tabulate column label legend. Coordinate Tab In this chapter.How clipboard actions can be used to import/export data from spreadsheet programs .

1) SIGUIJ U(2. Changing one will automatically change the other appropriately.y. SIGATM Orth Y coord. Orthogonal Y coord. Table Header HetroAtom Number Name Element Charge AltLoc Residue ChainID ResNum InsCode X Y Z B Occp U11 U22 U33 U12 U13 U23 SigX SigY SigZ SigB SigOccp SigU11 SigU22 SigU33 SigU12 SigU13 SigU23 x y z Full Name ATOM or HETATM Atom serial number Atom name Element Charge on the atom Alternate location Residue name Chain identifier Residue sequence number Insertion residue code Orthogonal X coord. SIGATM Temperature factor SIGATM Occupancy SIGUIJ U(1.2) SIGUIJ U(3.2) ANISOU U(3.3) ANISOU U(2.2) ANISOU U(1. Temperature factor Occupancy ANISOU U(1.3) SIGATM Orth X coord.3) Fractional x coord (Not in PDB) Fractional y coord (Not in PDB) Fractional z coord (Not in PDB) Data Type TRUE / FALSE Integer String (4 char max) String (2 char max) String (2 char max) Character String (3 char max) Character Integer Character Double Double Double Double Double Integer Integer Integer Integer Integer Integer Double Double Double Double Double Integer Integer Integer Integer Integer Integer Double Double Double 11 .1) ANISOU U(2. Orthogonal Z coord.y.Column Label Table TIP : The name information can be also accessed by opening “Search & Select” window and hovering mouse over the name you desire.z will NOT display anything intelligent if you don’t have spacegroup information.3) SIGUIJ U(1. Warning : Fractional x.Z are linked with fractional coordinates x.2) SIGUIJ U(1.z.Y.3) SIGUIJ U(2.3) ANISOU U(1. Warning : Orthogonal coordinates X. SIGATM Orth Z coord.

Changing Displayed Columns Open Change Column Displayed Dialog by Main menu : Option Æ Change Columns Displayed . 12 .Click on main toolbar button : Column Displayed Dialog Window You can select more than one column by CTRL key while left clicking mouse button to select. You can do other way by clicking left arrow button. Move columns from Inactive Columns to Columns Displayed by selecting them and clicking right arrow button to display them.

by selecting multiple atoms and typing “10” in Z will change Z values of all the coordinates to 10. For example. since it’s most likely that you will not hand type the all the coordinates manually when you select and edit. This is to utilize speed for most of the PDB editing operations. Values can be directly edited by typing in the value you desire. Warning : Data is changed by columns in all the coordinates selected in this program.Basic Coordinate Manipulation Data can be edited by moving the cursor around with a keyboard and mouse. 13 .

Basic selection can be further expedited by using a “Select” menu commands: One of the useful commands will be “Invert Selected Rows” (Ctrl + I). This will allow you to quickly change your selection when you use Search & Select commands: 14 .

Here is the answer and quick guide to the window: 15 . For example. but what happens when you need more selection power. when you want to lower the occupancy to 0. That’s when the “Search & Select” comes in handy.8 for all the non-water atoms with B factor greater than 40 but occupancy is set at 1.Advanced Coordinate Selection & Manipulation – “Search & Select” and “Edit Atom” Subwindows Basic manipulation is for a simple and quick manipulation. You can open the window by going to Main Menu: Search Æ Search & Select (Ctrl + F) or by clicking on the main toolbar: So how you do the example.

Allowed search values for HeteroAtoms are "TRUE" : checked for HeteroAtom "FALSE" : not checked for HeteroAtom Elaborating the example further. and InsertionCode. AlternateLocation. value must be enclosed in the quotation marks: “ “ These includes values for HetroAtom. ResidueType. Element. In here even the GUI column reference “HetroAtom” is ignored because the first search condition given is “B” 16 . Charge. ) = : Equal ! : Not equal > : Less than (Only applies to numbers) < : Greater than (Only applies to numbers) | : OR & : AND ^ : XOR For non-numbered values. Paranthesis are allowed (. AtomName. ChainID.So how do you write those search clauses? Here is a simple rule to the search clause syntax. This is exactly equivalent to above example. The search conditions meant : This exact condition can be also written in a single line IF you use the reference column names.

(B > 30 & Residue ! "HOH" ) | ( B > 80 & Residue = "HOH" ) This search clause will be selecting all atoms that are not HOH with B factor greater than 30 and HOH with B factors greater than 80.So how can you know all these column names rather than memorizing? Look at the “Select Columns” tab. but the secondary purpose is to give you hint to column names. 17 . Principal function of this tab is to control the columns selected when you press “Search & Select” button. You can also utilize the system for more complex search using parenthesis.

Edit Atom Subwindow You can search and select atoms. +. It will allow you edit the values of all the selected atoms simultaneously even allowing you to do simple arithmetic and column switching. 18 . ). Opening window : • • Open Main Menu : Edit Æ Edit Selected Atoms (Ctrl + E) Click on the main toolbar : Type in the values and press “Apply” to set the changes. You can also refer to other cells to do column switching. -. *. / are supported. You can refer to use the current value of the cell by typing “C”. Edit Atom window is the best way to do this. All the basic arithmetic like (. Now you want to edit multiple values in the atom.

y. Examples. Z respectively x. sU23. sU33 = Sigma anisotropic temperature factors These must be typed exactly with the correct case to make it work. Z = Orthogonal coordinate X. sz = Sigma fractional coordinate x. sU13. sY. You can also open more than one window of each. L:X = Last row’s orthogonal coordinate X L:L:U11 = Use two row above’s anisotropic temp factor U11 A3:N:O = Use next row of atom with Atom number 3’s occupancy Hint : You can open both “Search & Select” and “Edit Atom” windows at same time. Y. Y.This will switch x and y than shift z by 0. z respectively sB = Sigma temperature factor sO = Sigma occupancy sU11. sU22. U23. y. y. U12. z = Fractional coordinate x. U22. You can also do more complicated referencing: Row selection Keywords L = Go to last row N = Go to next row A#### = Go to atom number #### (ex. Y. U13. U33 = Anisotropic temperature factors sX. Z respectively sx.5 fractional coordinates. sZ = Sigma orthogonal coordinate X. sy. z respectively B = Temperature factor O = Occupancy U11. and row selection commands can be rigged multiple times. A130 = Atom with Atom number 130) Data selection Keywords X. sU12. 19 .

This can be used to directly import/export data from/to a spreadsheet program like MS Excel and OpenOffice Calc. Copy & Paste. You can copy by • • • • Main Menu : Edit Æ Copy Selected Cells (Ctrl + C) Main Toolbar : Main Menu : Edit Æ Paste (Ctrl + V) You can paste by Main Toolbar : 20 . These data are being transacted in a tab-delimited format.Coordinate Data Import & Export by Clipboard Action Simple clipboard actions are supported.

They can be used to transfer formatted text easily to new PDB files in the text editor or even between two PDB coordinates opened in two PDB Editor windows.Coordinate Data Import & Export in PDB Format by Clipboard Action Coordinate and space group information can be copy. cut. 21 . and pasted in PDB format.

22 .You can copy and cut in PDB format by • • • • Main Menu : Edit Æ Copy Selected Rows in PDB Format (Ctrl + Shift + C) Main Menu : Edit Æ Copy Spacegroup in PDB Format (Ctrl + Alt + Shift + C) Main Menu : Edit Æ Cut Selected Rows in PDB Format (Ctrl + X) Main Toolbar : Paste command is same as the tab-delimited data transaction.

Export data using clipboard actions . Secondary Structure Tab In this chapter.Add/Delete/Edit data in these tabs .Import/Export PDB formatted data using clipboard actions Table is divided into four columns • Class – Displays PDB Header • Entry – Displays entry number (IF the class is multi-entry) • Data Type – Shows what data the row represents • Value – Editable value of data (ONLY editable column) In the toolbar. Title/Remark. information about the row will be displayed in the format: (PDB Header) – (Data Type) : (Information on how data is organized) All the residue references should be formatted when you input or edit : (Residue) – (ChainID) – (Residue #) – (InsertionCode) ex. you will learn to . “GLY-B-100-C“ All the atom reference should be formatted : (AtomName) – (AlternateLocation) – (Residue) – (ChainID) – (Residue#) – (InsertionCode) TIP : Full data type name will be displayed by tooltip if you hover mouse over the table header 23 . Primary Structure.IV. • Green Plus signs are for adding new data • Red Minus signs are to remove from selected rows Functions will gray out. if it does not match the type or cannot be done In the main tooltip.

Copy command is same as in the coordinate window. but due to the data incompatibility by row tabulating the series of alternating data format made import process bug-prone and only a hassle to use it. Development of an import process had been attempted.Data Export in Tab-Delimited Format by Clipboard Action Unlike coordinate data. You can copy by • • Main Menu : Edit Æ Copy Selected Cells (Ctrl + C) Main Toolbar : 24 . data can only be exported in a tab-delimited format.

Copy and paste operations are identical to coordinate window manipulation. You can copy and cut in PDB format by • • • • Main Menu : Edit Æ Copy Selected Rows in PDB Format (Ctrl + Shift + C) Main Toolbar : Main Menu : Edit Æ Paste (Ctrl + V) You can paste by Main Toolbar : 25 .Data Import/Export in PDB Format Text by Clipboard Action Much like coordinate data. data can be imported/exported in the PDB format.

Changing the CCP4 Spacegroup # will also automatically update Spacegroup name. Coordinate Tools In this chapter.Extract protein sequence from SEQRES or ATOMs . you will learn to .Tabulate closest atom distances around a residue or selected point Editing Spacegroup. If the spacegroup is incorrect. residues. and vice versa.Systematically edit residue numbers and chain ID . and SCALE matrix Spacegroup.Generate symmetry mates and one cell figure .Rotate / translate atoms. 26 . and SCALE matrix can be edited by using Spacegroup Edit Window : Main Menu: Modify Æ Edit Spacegroup & Unitcell You can type in the appropriate values for each field. and chains . unit cell.Edit spacegroup and scale matrix . unit cell.V. it will keep give you warning message until you give an acceptable value.Edit CONECT records .Calculate number statistics of atoms .

however. Putting in 12 numbers will automatically parse as a matrix. This function will always favor to use a over b over c. alpha. You can also copy PDB formatted CRYST and SCALE text by : Main Menu : Edit Æ Copy Spacegroup in PDB Format (Ctrl +Alt + Shift + C) Pasting PDB Formatted text will also directly open up this window. SCALE matrix can be also edited manually. c. as well as. 27 . The values of orthogonal coordinates x. and gamma will turn RED if it doesn’t match the spacegroup. y. the labels a. You can always correct the matrix to the unitcell values by pressing Correct Cell Parameters button. The program will not care whether or not it’s correct compare to the unitcell.Unit cell parameters can be edited as anyway you want. beta. b. and z will depend on this matrix. alpha over beta over gamma when it forces. You can automatically force the convention by pressing the Correct Cell Parameters button.

You can change the values in the yellow cells. and your inputs will have a priority over the generated values. As you type in the values some of the rows will automatically turn yellow and values automatically filled base on the options you set. Residue Number Edit Option Description • Resolve conflict by increasing residue numbers 28 .Residue Number and Chain ID Editor Tool Residue number and chain ID can be easily and systematically edited using the subwindow tool: Main Menu : Modify Æ Edit Residue Number and Chain ID You can type in the values in New Chain ID and New Residue Number columns to change values. All the changes will NOT be in effect unless you press “Apply Changes” button.

For example. you can enter 4 in New Residue Number in a residue 3 row with this option which will automatically push residue 4 through 10 to 5 through 11. by changing the chain ID of ONLY the affected residues to new available one following the alphabet sequence. For example. • Synchronize residue number change to other chain if residue is same This option is when you have a dimer or higher oligomers separated in chains with same residue numbering. • Synchronize chain ID changes to all residues in the chain Changing one residue’s ID will automatically change the chain ID of all other residues in the chain.This option will automatically increase the number of residues that get conflicted by your input. when the change in ID will cause an overlap in the residue number. Chain ID Edit Option • Resolve conflict by changing chain ID automatically to available one This will resolve a conflict. if you have residue 1 through 10 and 12-20 and you want to put in new residue spot for 3. • Synchronize change in the chain This option will synchronize the change regardless of the conflict. if you have residues 20 through 30 and you set residue number 30 to 20 then it will automatically subtract 10 from all the residues in the chain. The program will automatically detect whether or not Residue is same and will try to synchronize the changes. This will be good for merging to chains. 29 . • Resolve conflict by shifting all affected Chain IDs This will resolve a conflict by changing the chain ID of ALL the residues in the other chain.

Atoms can be added by selecting rows from the Coordinate Window then pressing either 30 . playing with the CONECT records will have some use. Main Menu : Modify Æ Edit Atom Connectivity The tool’s main function is to automatically manage the bond pairs. if you have some special purpose. For example deleting CONECT record 1Æ2 will also automatically removed 2Æ1.Editing CONECT records Although very rarely used. This tool is to help you automatically manage CONECT record editing.

Deleting bond can be done by selecting a single bond by clicking any rows in Bond # columns then pressing Deleting entire center with all the bonds formed from that center can be done by selecting a row and pressing 31 .

Forcing the fractional boundary does have 32 .Generating Symmetry Mates and Exact One Fractional Coordinate Cells Symmetry operations can be done easily by using Generate Symmetry Mates tool. You can open that window by : Main Menu : Calculate Æ Generate Symmetry Mates All the checked symmetry operations will be generated after pressing “Generate” button. Although this does not have much utility because many modeling program has the symmetry generation option. Chain IDs can be manually typed into the user’s like. Above example is default generated which tries to use the next available or unused alphabet or ASCII character. this tool is developed for quickly forcing all the coordinates within the fractional coordinate boundary 0 to 1.

Some crude breaks in the disulfide bonds are formed but good enough for a quick empirical evaluation of the available space in the unit cell.some utility when you do molecular replacement of fragments to quickly check available empty space in the unitcell. Below is an example of PDB 1A7S modeled in Coot 0.3. 33 . This will help you to figure out whether or not there is a space available for the next molecules to fit in.3 after all symmetry mates were generated by the editor within the fractional coordinate 0 to 1.

34 . One of the labels will turn red and Calculated Transformation Matrix will show up as you input your values. You can open this tool subwindow by : Main Menu : Calculate Æ Rotate / Translate Atoms Operations can be typed in the first text field. this tool tries to specialize itself by allowing you to do operations selectively and quickly. You have to press “Transform” button to do the operation. Quick part comes in by you type in the numbers or directly cut & pasting number in other formats to get quickly parsed for the operation.Rotate / Translate Selected Atoms One of the basic functions available in most other programs. Selective part comes in by allowing you to rotate/translate by moving or copying only the selected atoms from the Coordinate Window.

You can open this window by • • Main Menu : Calculate Æ Calculate Number Statistics Main Toolbar : Max Atom / Min Atom values are referencing to the atom number of records that gives max / min value. maximum. 35 . and minimum of various numerical values in ATOM / HETATM information can be directly extracted from all AND selected sequences in the coordinate window.Extracting Coordinate Statistics Statistics like average. The table values can be also copied into the clipboard by (Ctrl + C) and paste it into the spreadsheet in the table format. standard deviation.

36 . You can open this window by • • Main Menu : Calculate Æ Extract Sequence Main Toolbar : The output values can be copied onto the clipboard by selecting the text you want to copy and pressing Ctrl + C. or directly derived from ATOM / HETATM coordinates.Extracting Protein Sequence from SEQRES or ATOM / HETATM Protein sequence can be extracted in a FASTA or three letter PDB residue format from the secondary structure records if available.

or coordinate points. 37 . This is a simple quick tool for tabulating the distance around interesting residues. like possible ligand binding sites. Distances will be calculated by pressing “Calculate” button. You can open window by : Main Menu : Calculate Æ Find Closest Atom Distances Search point atoms can be selected by selecting the atoms you want from the Coordinate Window. like ligands.Tabulating closest atom distances around atoms or defined coordinates Editor also has a simple tool for tabulating the distance around selected atoms or defined coordinate points.

Exact operation of all the other operations can be found in the Generate Symmetry Mates window – Symmetry Operations table. You can sort by clicking on the column header. The operation number should be read as starting 0 on the first row with the identity operator then subsequently incrementing in 1 as you go down the rows. Symmetry operator number reflects which symmetry operation had to be done to get the atom within the search distance limit. The sorted column will display arrow like the column header “Distance” is showing in the above example. Pressing the same column again will change the sort direction. 38 . Data can be also copied onto the clipboard by selecting the cells you want to copy and pressing Ctrl + C.Distance results comes out like the one below : Data comes out in an unsorted fashion. 0 is always identity operator.

with no transfer of a copy. we are referring to freedom. so that their problems will not be attributed erroneously to authors of previous versions. States should not allow patents to restrict development and use of software on general-purpose computers. we stand ready to extend this provision to those domains in future versions of the GPL. except executing it on a computer or modifying a private copy. that licensees may convey the work under this License. every program is threatened constantly by software patents. copyleft license for software and other kinds of works. you must pass on to the recipients the same To "convey" a work means any kind of propagation that enables other freedoms that you received. Inc. but changing it is not allowed. Therefore. free programs. Finally. too. TERMS AND CONDITIONS 0. distribution (with or without modification). whether gratis or for a fee. it applies also to "recipients" may be individuals or organizations. We. we wish to An interactive user interface displays "Appropriate Legal Notices" to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice. Preamble The GNU General Public License is a free. For the developers' and authors' protection. Some devices are designed to deny users access to install or run modified versions of the software inside them. or. avoid the special danger that patents applied to a free program could make it effectively proprietary. but which is not part of that Major Component. too. The licenses for most software and other practical works are designed "Copyright" also means copyright-like laws that apply to other kinds of to take away your freedom to share and change the works. the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free "The Program" refers to any copyrightable work licensed under this software for all its users. and in some countries other activities as well. although the manufacturer can do so. If such problems arise substantially in other domains. The systematic pattern of such abuse occurs in the area of products for individuals to> Everyone is permitted to copy and distribute verbatim copies of this license document. You must make sure that they. The precise terms and conditions for copying. and that you know you can do these things. To prevent this. To "modify" a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission. that you can change the software or use pieces of it in new on the Program. Propagation includes copying. To protect your rights. the GPL assures that patents cannot be used to render the program non-free. the GPL requires that modified versions be marked as changed. in the case of interfaces specified for a particular programming language. A "Standard Interface" means an interface that either is an official standard defined by a recognized standards body. The "System Libraries" of an executable work include anything. would make you directly or secondarily liable for infringement under applicable copyright law.GNU GENERAL PUBLIC LICENSE Version 3. such as a menu. the Free Software Foundation. or if you modify it: responsibilities to respect the freedom of others. use the License. you have certain responsibilities if you distribute copies of the software. that you receive source code or can get it if you A "covered work" means either the unmodified Program or a work based want it. is not conveying. as needed to protect the freedom of users. Our General Public Licenses are designed to make sure that you earlier work or a work "based on" the earlier work. receive parties to make or receive copies. And you must show them these terms so they a computer network. For both users' and authors' sake. The resulting work is called a "modified version" of the price. making available to the public. works. one that is widely used among developers working in that language. 1. which is precisely where it is most unacceptable. we have designed this version of the GPL to prohibit the practice for those products. Source Code. and how to view a copy of this License. and (b) serves only to enable use of the work with that 39 . The "source code" for a work means the preferred form of the work for making modifications to it. and (2) offer you this License giving you legal permission to copy. Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software. "Licensees" and GNU General Public License for most of our software. "This License" refers to version 3 of the GNU General Public License. that (a) is included in the normal form of packaging a Major Component. and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided). other than the making of an When we speak of free software. You can apply it to your programs. without permission. have the freedom to distribute copies of free software (and charge for them if you wish). any other work released this way by its authors. Mere interaction with a user through or can get the source code. "Object code" means any non-source form of a work. By contrast. but in those that do. <http://fsf. This is fundamentally incompatible with the aim of protecting users' freedom to change the software. such as semiconductor masks. know their rights. a prominent item in the list meets this criterion. distribute and/or modify it. Each licensee is addressed as "you". we need to prevent others from denying you these rights or asking you to surrender the rights. the GPL clearly explains that there is no warranty for this free software. if you distribute copies of such a program. 29 June 2007 Copyright (C) 2007 Free Software Foundation. For example. To "propagate" a work means to do anything with it that. Therefore. other than the work as a whole. Definitions. If the interface presents a list of user commands or options. distribution and modification follow. not exact copy.

provided that you also meet all of these conditions: a) The work must carry prominent notices stating that you modified it. Conveying Modified Source Versions. provided that you comply with the terms of this License in conveying all material for which you do not control copyright. and all its parts. under this License to anyone who comes into possession of a copy. This License will therefore apply. in this context. Corresponding Source includes interface definition files associated with source files for the work. or general-purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work. A "Major Component". is called an "aggregate" if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation's users beyond what the individual works permit. Conveying under any other circumstances is permitted solely under the conditions stated below. d) If the work has interactive user interfaces. The output from running a covered work is covered by this License only if the output. accompanied by a 40 . No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996. You may convey a covered work in object code form under the terms of sections 4 and 5. regardless of how they are packaged. you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work. in one of these ways: a) Convey the object code in. You may convey a work based on the Program. The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source. The "Corresponding Source" for a work in object code form means all the source code needed to generate. and give all recipients a copy of this License along with the Program. provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice. or to implement a Standard Interface for which an implementation is available to the public in source code form. 5. or embodied in. 2. or similar laws prohibiting or restricting circumvention of such measures. along with any applicable section 7 additional terms. in the form of source code under the terms of section 4. Protecting Users' Legal Rights From Anti-Circumvention Law. Basic Permissions. c) You must license the entire work. a physical product (including a physical distribution medium). You may make. However. in or on a volume of a storage or distribution medium. however. constitutes a covered work. and you may offer support or warranty protection for a fee. install. Conveying Non-Source Forms. Those thus making or running the covered works for you must do so exclusively on your behalf. a physical product (including a physical distribution medium). but it does not invalidate such permission if you have separately received it. your work need not make them do so. means a major essential component (kernel. This License gives no permission to license the work in any other way. and so on) of the specific operating system (if any) on which the executable work runs. in any medium. section 10 makes it unnecessary. including scripts to control those activities. against the work's users. This License explicitly affirms your unlimited permission to run the unmodified Program. Sublicensing is not allowed. and you disclaim any intention to limit operation or modification of the work as a means of enforcing. For example. The Corresponding Source for a work in source code form is that same work. b) Convey the object code in. Conveying Verbatim Copies. You may charge any price or no price for each copy that you convey. keep intact all notices of the absence of any warranty. run and propagate covered works that you do not convey. or provide you with facilities for running those works. and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require. your or third parties' legal rights to forbid circumvention of technological measures. 6. keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code. b) The work must carry prominent notices stating that it is released under this License and any conditions added under section 7. on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you. such as by intimate data communication or control flow between those subprograms and other parts of the work. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you. 3.Major Component. to the whole of the work. window system. This License acknowledges your rights of fair use or other equivalent. This requirement modifies the requirement in section 4 to "keep intact all notices". and are irrevocable provided the stated conditions are met. under your direction and control. as a whole. which are not by their nature extensions of the covered work. as provided by copyright law. or embodied in. When you convey a covered work. or a compiler used to produce the work. given its content. each must display Appropriate Legal Notices. without conditions so long as your license otherwise remains in force. provided that you also convey the machine-readable Corresponding Source under the terms of this License. or the modifications to produce it from the Program. or an object code interpreter used to run it. and which are not combined with it such as to form a larger program. it does not include the work's System Libraries. and giving a relevant date. and (for an executable work) run the object code and to modify the work. accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange. 4. All rights granted under this License are granted for the term of copyright on the Program. if the Program has interactive interfaces that do not display Appropriate Legal Notices. You may convey verbatim copies of the Program's source code as you receive it. A compilation of a covered work with other separate and independent works. Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate.

c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source. you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms: a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License. or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. and Installation Information provided. the product. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made. on a durable physical medium customarily used for software interchange. or requiring that modified versions of such material be marked in reasonable ways as different from the original version. for any liability that these contractual assumptions directly impose on those licensors and authors. If additional permissions apply only to part of the Program. which means any tangible personal property which is normally used for personal. or d) Limiting the use for publicity purposes of names of licensors or authors of the material. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License. and only if you received the object code with such an offer. for which you have or can give appropriate copyright permission. This alternative is allowed only occasionally and noncommercially. reading or copying. procedures. or f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient. e) Convey the object code using peer-to-peer transmission. "normally used" refers to a typical or common use of that class of product. the work has been installed in ROM). you remain obligated to ensure that it is available for as long as needed to satisfy these requirements. industrial or non-consumer uses. If you convey an object code work under this section in. provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d. A "User Product" is either (1) a "consumer product". family. For a particular product received by a particular user. "Installation Information" for a User Product means any methods.written offer. and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a All other non-permissive additional terms are considered "further fixed term (regardless of how the transaction is characterized). that part may be used separately under those permissions. to the extent that they are valid under applicable law. authorization keys. for material you add to a covered work. or (2) anything designed or sold for incorporation into a dwelling. need not be included in conveying the object code work. in accord with subsection 6b. or b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it. and offer equivalent access to the Corresponding Source in the same way through the same place at no further charge. or any part of it. If the Program as you received it. but the entire Program remains governed by this License without regard to the additional permissions. provided you maintain clear directions next to the object code saying where to find the Corresponding Source. or expects or is expected to use. But this requirement does not apply 41 . valid for at least three years and valid for as long as you offer spare parts or customer support for that product model. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network. If the place to copy the object code is a network server. A separable portion of the object code. Corresponding Source conveyed. added by you to a covered work. d) Convey the object code by offering access from a designated place (gratis or for a charge). or service marks. warranty. contains a notice stating that it is by the Installation Information. or household purposes. or for the User Product in which it has been modified or installed. A product is a consumer product regardless of whether the product has substantial commercial. The requirement to provide Installation Information does not include a requirement to continue to provide support service. Additional Terms. whose source code is excluded from the Corresponding Source as a System Library. the Corresponding Source may be on a different server (operated by you or a third party) that supports equivalent copying facilities. (Additional permissions may be written to require their own removal in certain cases when you modify the work. 7. trademarks. and must require no special password or key for unpacking. doubtful cases shall be resolved in favor of coverage. regardless of the status of the particular user or of the way in which the particular user actually uses. in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form). or with. or updates for a work that has been modified or installed by the recipient. you may at your option remove any additional permissions from that copy. "Additional permissions" are terms that supplement the terms of this License by making exceptions from one or more of its conditions. or specifically for use in. the Corresponding Source conveyed under this section must be accompanied restrictions" within the meaning of section 10. or c) Prohibiting misrepresentation of the origin of that material. When you convey a copy of a covered work. for a price no more than your reasonable cost of physically performing this conveying of source. to give anyone who possesses the object code either (1) a copy of the Corresponding Source for all the software in the product that is covered by this License. Notwithstanding any other provision of this License.) You may place additional permissions on material. or (2) access to copy the Corresponding Source from a network server at no charge. a User Product. You need not require recipients to copy the Corresponding Source along with the object code. unless such uses represent the only significant mode of use of the product. or from any part of it. if neither you nor any third party retains the ability to install modified object code on the User Product (for example. Regardless of what server hosts the Corresponding Source. In determining whether a product is a consumer product. or e) Declining to grant rights under trademark law for use of some trade names.

however denominated. or importing the Program or any portion of it. nothing other than this License grants you permission to propagate or modify any covered work. or merging organizations. You are not responsible for enforcing compliance by third parties with this License. propagate. or (2) arrange to deprive yourself of the benefit of the patent license for this particular work. Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. To "grant" such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party. The work thus licensed is called the contributor's "contributor version". provided that the further restriction does not survive such relicensing or conveying. If you add terms to a covered work in accord with this section. modify or convey a specific copy of the covered work. in the relevant source files. a "patent license" is any express agreement or commitment. An "entity transaction" is a transaction transferring control of an organization. you may add to a covered work material governed by the terms of that license document. However. permitted by this License. you do not qualify to receive new licenses for the same material under section 10. In the following three paragraphs. Moreover. A contributor's "essential patent claims" are all patent claims owned or controlled by the contributor. or selling its contributor version. Automatic Licensing of Downstream Recipients. you may not impose a license fee. but do not include claims that would be infringed only as a consequence of further modification of the contributor version. "control" includes the right to grant patent sublicenses in a manner consistent with the requirements of this License. selling. you may remove that term. if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation. using. or (3) arrange. Therefore. You may not propagate or modify a covered work except as expressly provided under this License. prohibits the exercise of. and the Corresponding Source of the work is not available for anyone to copy. would infringe one or more identifiable patents in that country that you have reason to believe are valid. if the predecessor has it or can get it with reasonable efforts. unless and until the copyright holder explicitly and finally terminates your license. this is the first time you have received notice of violation of this License (for any work) from that copyright holder. Termination. or propagate by procuring conveyance of. a statement of the additional terms that apply to those files. A patent license is "discriminatory" if it does not include within the scope of its coverage. 11. 8. you indicate your acceptance of this License to do so. and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11). each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph. Acceptance Not Required for Having Copies. offer for sale. and (b) permanently.governed by this License along with a term that is a further restriction. the above requirements apply either way. of making. sell. Any attempt otherwise to propagate or modify it is void. if you cease all violation of this License. However. If your rights have been terminated and not permanently reinstated. you must place. to extend the patent license to downstream recipients. Each contributor grants you a non-exclusive. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. royalty. that would be infringed by some manner. by modifying or propagating a covered work. a covered work. or is 42 . or stated as exceptions. using. Patents. 9. through a publicly available network server or other readily accessible means. If propagation of a covered work results from an entity transaction. These actions infringe copyright if you do not accept this License. not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). If you convey a covered work. For purposes of this definition. modify and propagate the contents of its contributor version. permissive or non-permissive. worldwide. A "contributor" is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. royalty-free patent license under the contributor's essential patent claims. to make. then the patent license you grant is automatically extended to all recipients of the covered work and works based on it. your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means. Additional terms. or substantially all assets of one. use. Each time you convey a covered work. For example. knowingly relying on a patent license. whether already acquired or hereafter acquired. You are not required to accept this License in order to receive or run a copy of the Program. then your license from a particular copyright holder is reinstated (a) provisionally. modify and propagate that work. pursuant to or in connection with a single transaction or arrangement. 10. You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. or your recipient's use of the covered work in a country. or subdividing an organization. If a license document contains a further restriction but permits relicensing or conveying under this License. "Knowingly relying" means you have actual knowledge that. then you must either (1) cause the Corresponding Source to be so available. may be stated in the form of a separately written license. import and otherwise run. but for the patent license. you convey. and grant a patent license to some of the parties receiving the covered work authorizing them to use. offering for sale. to run. your conveying the covered work in a country. in a manner consistent with the requirements of this License. free of charge and under the terms of this License. plus a right to possession of the Corresponding Source of the work from the predecessor in interest. and you cure the violation prior to 30 days after your receipt of the notice. or other charge for exercise of rights granted under this License. If. or a notice indicating where to find the applicable terms. the recipient automatically receives a license from the original licensors. subject to this License. and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making.

prior to 28 March 2007. the best way to achieve this is to make it Foundation. 15. the Free Software Foundation. to any of the parties who would receive the covered work from you. you have SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY permission to link or combine any covered work with a work licensed OTHER PROGRAMS). The terms of this THE POSSIBILITY OF License will continue to apply to the part which is the covered work. then as a consequence you may MODIFIES AND/OR CONVEYS not convey it at all. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. but may differ in detail to copy of the Program in return for a fee. concerning interaction through a network will apply to the 17. or that patent license was granted. THERE IS NO WARRANTY FOR THE PROGRAM. and each file should have at least versions of the GNU General Public License can be used. It is safest to attach them to the start of each source file to most effectively If the Program specifies that a proxy can decide which future state the exclusion of warranty. If you cannot convey a TO IN WRITING covered work so as to satisfy simultaneously your obligations under this WILL ANY COPYRIGHT HOLDER. Use with the GNU Affero General Public License. they do not IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED excuse you from the conditions of this License. Interpretation of Sections 15 and 16. SHOULD THE PROGRAM PROVE DEFECTIVE. and to convey the resulting work. and you want it to be of the greatest version or of any later version published by the Free Software possible use to the public. that proxy's public statement of acceptance of a version permanently authorizes you the "copyright" line and a pointer to where the full notice is found. THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. if you agree to terms that obligate you THE PROGRAM AS PERMITTED ABOVE. Disclaimer of Warranty. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software. To do so. Such new versions will an absolute waiver of all civil liability in connection with the Program. and under which the third party grants. However. reviewing courts shall apply local law that most closely approximates The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. combination as such. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms. Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law. or 43 . For example. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND. INCLUDING. Limitation of Liability. SUCH DAMAGES.conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies). either version 3 of the License. LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES Notwithstanding any other provision of this License. you have the option of following the terms and conditions either of that numbered If you develop a new program. INCIDENTAL OR CONSEQUENTIAL DAMAGES License would be to refrain entirely from conveying the Program. to choose that version for the Program. <one line to give the program's name and a brief idea of what it does. agreement or otherwise) that contradict the conditions of this License. INCLUDING ANY the Program. section 13. 16. YOU ASSUME THE COST OF ALL NECESSARY SERVICING. address new problems or concerns. the only way you could satisfy both those terms and this GENERAL. EITHER EXPRESSED OR IMPLIED. If conditions are imposed on you (whether by court order. by the Free Software Foundation. Revised Versions of this License. no additional obligations are imposed on any This program is free software: you can redistribute it and/or modify author or copyright holder as a result of your choosing to follow a it under the terms of the GNU General Public License as published by later version. or (b) primarily for and in connection with specific products or compilations that contain the covered work. under which you make payment to the third party based on the extent of your activity of conveying the work. BE LIABLE TO YOU FOR to collect a royalty for further conveying from those to whom you convey DAMAGES. If the Program does not specify a version number of the GNU General Public License. you may choose any version ever published free software which everyone can redistribute and change under these terms. ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT 13. TO THE EXTENT PERMITTED BY APPLICABLE LAW. No Surrender of Others' Freedom. unless you entered into that arrangement. 12. attach the following notices to the program. OR ANY OTHER PARTY WHO License and any other pertinent obligations. SPECIAL. BUT NOT LIMITED TO. but the special requirements of the GNU Affero General Public License. under version 3 of the GNU Affero General Public License into a single EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF combined work. If the Program specifies that a certain numbered version of the GNU General How to Apply These Terms to Your New Programs Public License "or any later version" applies to it. REPAIR OR CORRECTION.> Copyright (C) <year> <name of author> Later license versions may give you additional or different permissions. 14. unless a warranty or assumption of liability accompanies a be similar in spirit to the present version. END OF TERMS AND CONDITIONS Each version is given a distinguishing version number.

see <http://www. <http://www. if necessary. make it output a short notice like this when it starts in an interactive mode: into proprietary programs. If this is what you want to 44 . without even the implied warranty of parts of the General Public License. Of course. If your program is a subroutine library. along with this program. For more information on this. GNU General Public License for more details. If not. You should also get your employer (if you work as a programmer) or school. for a GUI interface. for details typPublic e `show License instead of this License. to sign a "copyright disclaimer" for the program. please read w'.org/licenses/>. Also add information on how to contact you by electronic and paper mail.(at your option) any later version. you may consider it more useful to permit linking proprietary applications with <program> Copyright (C) <year> <name of author> the library. The hypothetical commands `show w' and `show c' should show the This program is distributed in the hope that it will be useful. See might the be different. type `show c' for details. use the GNU Lesser General This program comes with ABSOLUTELY NO>. and how to apply and follow the GNU GPL. your program's commands MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. This is free software. see <http://www. and you are welcome to redistribute it under certain conditions. You should have received a copy of the GNU General Public License if any.html>. you would use an "about box". The GNU General Public License does not permit incorporating your program If the program does terminal interaction.gnu.gnu. But first. appropriate but WITHOUT ANY WARRANTY.gnu.