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.


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. you are suppose to enter “gedit . Select PDB_Editor. <Your Shell Name> is anything that follows “/bin/” Therefore if you see.Making shortcut in Windows 1) Right clicking on the desktop.jar file>” Tcsh & Csh : alias pdbeditor ‘java – har <Full path of PDB_Editor. 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 . 2) Select “New” Æ “Shortcut” 3) Click “Browse”. 5 . and click “Finish” 6) OPTIONAL : You can put it in the Start menu or Quicklaunch by dragging it into it. “/bin/bash” in #1.jar file. and click “OK” 4) Follow the screenshot below by typing “javaw –jar” in front of the displayed filename.<Your Shell Name>rc” There is a period “. 5) Click “Next” Give appropriate name.jar file>’ 5) Now you can type in “pdbeditor <Filename>” in Terminal to run the editor.” before your shell name.

6 . as well as.II. All the buttons in the toolbar has tooltip function. you will learn to .Give brief summary of each commands in the Main Menu It’s very common GUI window. Main Window In this chapter. Nothing really interesting to discuss about. temporary function tip will be displayed in the statusbar when you place mouse over it.Label key components in the main 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. 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. “All Atoms” – process all rows • Select – Ways to quickly search & select specific records 7 .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.

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. 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.o Search and Select Window – Main coordinate search window o Invert selections – Stop selecting rows that are currently selected. undo/redoable operation so utilize it without hesitation • Calculate o Generate symmetry mates o Rotate and translate atoms 8 . 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.

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

How atom data is manipulated by mouse & keyboard . and how to change columns displayed .III.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 . Coordinate Tab In this chapter.How clipboard actions can be used to import/export data from spreadsheet programs .Tabulate column label legend.How to effectively manipulate atoms using “Search and Select” and “Edit Atom” window .

Orthogonal Z coord. Warning : Fractional x.2) SIGUIJ U(3. Orthogonal Y coord.Y.y. SIGATM Temperature factor SIGATM Occupancy SIGUIJ U(1.y. Warning : Orthogonal coordinates X.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 . 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.2) ANISOU U(3.1) SIGUIJ U(2.1) ANISOU U(2. SIGATM Orth Z coord.3) ANISOU U(1.Column Label Table TIP : The name information can be also accessed by opening “Search & Select” window and hovering mouse over the name you desire. SIGATM Orth Y coord.z will NOT display anything intelligent if you don’t have spacegroup information.3) SIGUIJ U(2.2) SIGUIJ U(1.3) SIGUIJ U(1.3) ANISOU U(2.3) SIGATM Orth X coord.z.2) ANISOU U(1. Changing one will automatically change the other appropriately.Z are linked with fractional coordinates x. Temperature factor Occupancy ANISOU U(1.

12 . You can do other way by clicking left arrow button.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. Move columns from Inactive Columns to Columns Displayed by selecting them and clicking right arrow button to display them.Changing Displayed Columns Open Change Column Displayed Dialog by Main menu : Option Æ Change Columns Displayed .

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

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 .

when you want to lower the occupancy to 0. but what happens when you need more selection power. That’s when the “Search & Select” comes in handy.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. Here is the answer and quick guide to the window: 15 .8 for all the non-water atoms with B factor greater than 40 but occupancy is set at 1. For example.

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

but the secondary purpose is to give you hint to column names.So how can you know all these column names rather than memorizing? Look at the “Select Columns” tab. You can also utilize the system for more complex search using parenthesis. 17 . Principal function of this tab is to control the columns selected when you press “Search & Select” button. (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.

).Edit Atom Subwindow You can search and select atoms. You can also refer to other cells to do column switching. Edit Atom window is the best way to do this. Now you want to edit multiple values in the atom. -. All the basic arithmetic like (. You can refer to use the current value of the cell by typing “C”. +. / are supported. 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.

5 fractional coordinates. and row selection commands can be rigged multiple times. sZ = Sigma orthogonal coordinate X. You can also open more than one window of each. Examples. Y.This will switch x and y than shift z by 0. z = Fractional coordinate x. sU13. Y. z respectively sB = Sigma temperature factor sO = Sigma occupancy sU11. y. U12. Z respectively sx. U22. 19 . U13. Z respectively x. z respectively B = Temperature factor O = Occupancy U11. sU12. y. Z = Orthogonal coordinate X. sz = Sigma fractional coordinate x. sy. y. sY. 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. A130 = Atom with Atom number 130) Data selection Keywords X. 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. sU33 = Sigma anisotropic temperature factors These must be typed exactly with the correct case to make it work. sU22. U23. U33 = Anisotropic temperature factors sX. sU23. Y.

Coordinate Data Import & Export by Clipboard Action Simple clipboard actions are supported. Copy & Paste. These data are being transacted in a tab-delimited format. 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 . This can be used to directly import/export data from/to a spreadsheet program like MS Excel and OpenOffice Calc.

cut.Coordinate Data Import & Export in PDB Format by Clipboard Action Coordinate and space group information can be copy. 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. 21 . and pasted in PDB format.

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. 22 .

“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 .Export data using clipboard actions . Primary Structure. Secondary Structure Tab In this chapter.Add/Delete/Edit data in these tabs . 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.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. you will learn to . • 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.IV.

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. Copy command is same as in the coordinate window. You can copy by • • Main Menu : Edit Æ Copy Selected Cells (Ctrl + C) Main Toolbar : 24 .Data Export in Tab-Delimited Format by Clipboard Action Unlike coordinate data. Development of an import process had been attempted. 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.

V. unit cell. 26 . Changing the CCP4 Spacegroup # will also automatically update Spacegroup name. and SCALE matrix Spacegroup.Tabulate closest atom distances around a residue or selected point Editing Spacegroup.Systematically edit residue numbers and chain ID . it will keep give you warning message until you give an acceptable value.Edit spacegroup and scale matrix .Generate symmetry mates and one cell figure . 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.Edit CONECT records . and vice versa.Extract protein sequence from SEQRES or ATOMs .Calculate number statistics of atoms . you will learn to . If the spacegroup is incorrect. unit cell. and chains . Coordinate Tools In this chapter. residues.Rotate / translate atoms.

beta. 27 . alpha. c. Putting in 12 numbers will automatically parse as a matrix. 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. and gamma will turn RED if it doesn’t match the spacegroup. however. SCALE matrix can be also edited manually. The values of orthogonal coordinates x. as well as. the labels a. alpha over beta over gamma when it forces. b. The program will not care whether or not it’s correct compare to the unitcell. You can automatically force the convention by pressing the Correct Cell Parameters button. You can always correct the matrix to the unitcell values by pressing Correct Cell Parameters button.Unit cell parameters can be edited as anyway you want. This function will always favor to use a over b over c. y. and z will depend on this matrix.

All the changes will NOT be in effect unless you press “Apply Changes” button. and your inputs will have a priority over the generated values. Residue Number Edit Option Description • Resolve conflict by increasing residue numbers 28 . You can change the values in the yellow cells. 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 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.

• Synchronize change in the chain This option will synchronize the change regardless of the conflict. • 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. Chain ID Edit Option • Resolve conflict by changing chain ID automatically to available one This will resolve a conflict. • 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. when the change in ID will cause an overlap in the residue number. 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. For example. 29 . by changing the chain ID of ONLY the affected residues to new available one following the alphabet sequence. The program will automatically detect whether or not Residue is same and will try to synchronize the changes. 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.This option will automatically increase the number of residues that get conflicted by your input. For example. • 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. if you have residue 1 through 10 and 12-20 and you want to put in new residue spot for 3. This will be good for merging to chains.

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

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 .

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

Below is an example of PDB 1A7S modeled in Coot 0. This will help you to figure out whether or not there is a space available for the next molecules to fit in. 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. 33 .3.3 after all symmetry mates were generated by the editor within the fractional coordinate 0 to 1.

34 .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. One of the labels will turn red and Calculated Transformation Matrix will show up as you input your values. 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. You can open this tool subwindow by : Main Menu : Calculate Æ Rotate / Translate Atoms Operations can be typed in the first text field.

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. 35 . standard deviation. 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. and minimum of various numerical values in ATOM / HETATM information can be directly extracted from all AND selected sequences in the coordinate window. maximum.

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. 36 .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 directly derived from ATOM / HETATM coordinates.

37 . 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.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. This is a simple quick tool for tabulating the distance around interesting residues. like ligands. like possible ligand binding sites. or coordinate points.

38 .Distance results comes out like the one below : Data comes out in an unsorted fashion. 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. 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. 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. Data can be also copied onto the clipboard by selecting the cells you want to copy and pressing Ctrl + C. 0 is always identity operator. Pressing the same column again will change the sort direction.

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