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<html> <head> <title>MayaChemTools:Documentation:ModifyPDBFiles.pl</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <tr align="left" valign="top"><td width="33%" align="left"><a href="./ModifyNewLineChar.html" title="ModifyNewLineChar.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ModifySDFilesDataFields.html" title="ModifySDFilesDataFields.html">Next</a></td><td width="34%" align="middle"><strong>ModifyPDBFiles.pl</strong></td><td width="33%" align="right"><a href="././code/ModifyPDBFiles.html" title="View source code">Code</a> | <a href="./../pdf/ModifyPDBFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ModifyPDBFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ModifyPDBFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ModifyPDBFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> </table> </div> <p> </p> <h2>NAME</h2> <p>ModifyPDBFiles.pl - Modify data in PDBFile(s)</p> <p> </p> <h2>SYNOPSIS</h2> <p>ModifyPDBFiles.pl PDBFile(s)...</p> <p>ModifyPDBFiles.pl [<strong>-a, --AtomNumberStart</strong> number] [<strong>-c, --ChainIDStart</strong> character] [<strong>--ChainIDRenameEmpty</strong> yes | no] [<strong>-h, --help</strong>] [<strong>-k, --KeepOldRecords</strong> yes | no] [<strong>-m, --mode </strong> RenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs] [<strong>--ModifyHeader</strong> yes | no] [<strong>-o, --overwrite</strong>] [<strong>--ResidueNumberMode</strong> Sequential | PerChain] [<strong>--ResidueNumberStart</strong> number] [<strong>--ResidueNumberHetatmMode</strong> automatic | specify] [<strong>--ResidueNumberStarHetatm</strong> number] [<strong>-r, --root</strong> rootname] [<strong>--WaterResidueNames</strong> Automatic | "ResidueName, [ResidueName,...]"] [<strong>--WaterResidueStart</strong> number] [<strong>-w, --WorkingDir</strong> dirname] PDBFile(s)...</p> <p> </p> <h2>DESCRIPTION</h2> <p>Modify data in <em>PDBFile(s)</em>: renumber atoms, residues, and water residues or assign new chain IDs. Multiple PDBFile names are separated by spaces. The valid file extension is <em>.pdb</em>. All other file name extensions are ignored during the wild card expansion. All the PDB files in a current directory can be specified either by <em>*.pdb</em> or the current directory name.</p> <p> </p> <h2>OPTIONS</h2> <dl> <dt><strong><strong>-a, --AtomNumberStart</strong> <em>number</em></strong></dt> <dd> <p>Starting atom number to use during <em>RenumberAtoms</em> value of <strong>-m, --mode</strong> option. Default: <em>1</em>. Valid values: positive integers.</p> </dd> <dt><strong><strong>-c, --ChainIDStart</strong> <em>character</em></strong></dt> <dd> <p>A single character to use for starting IDs for chains during <em>RenameChainIDs</em> value of <strong>-m, --mode</strong> option. Default: <em>A</em>. Valid values: <em>A to Z</em>.</p> </dd> <dt><strong><strong>--ChainIDRenameEmpty</strong> <em>Yes | No</em></strong></dt> <dd> <p>Specify whether to rename empty chain IDs during <em>RenameChainIDs</em> <strong>-m, --mode</strong> value. By default, ATOM and HETATM records with no chain IDs are left unchanged. Possible values: <em>yes | no</em>. Default: <em>No</em>.</p> </dd> <dt><strong><strong>-h, --help</strong></strong></dt> <dd> <p>Print this help message.</p> </dd> <dt><strong><strong>-k, --KeepOldRecords</strong> <em>yes | no</em></strong></dt> <dd> <p>Specify whether to transfer old non ATOM and HETATM records from input PDBFile(s) to new PDBFile(s). By default, except for the HEADER record, all records other than ATOM/HETATM are dropped during the generation of new PDB files. Possible values: <em>yes | no</em>. Default: <em>no</em>.</p> </dd> <dt><strong><strong>-m, --mode </strong> <em>RenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs</em></strong></dt> <dd> <p>Specify how to modify <em>PDBFile(s)</em>. Possible values: <em>RenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs</em>. Default: <em>RenumberResidues</em>.</p> <p>For <em>RenumberAtoms</em> mode, residue number in ATOM and HETATM records are reassigned sequentially starting using value of <strong>-a, --AtomNumberStart</strong> option.</p> <p>For <em>RenumberResidues</em> mode, serial number in ATOM and HETATM records are reassigned either sequentially or statring from specified values for ATOM and HETATM records in each chain.</p> <p>For <em>RenumberWaters</em> mode, residue number for waters are reassigned starting from a specific value.</p> <p>For <em>RenameChainIDs</em> mode, all the chain IDs are reassigned starting from a specific chain ID.</p> <p>During the generation of new PDB files, unnecessary CONECT records are dropped.</p> </dd> <dt><strong><strong>--ModifyHeader</strong> <em>yes | no</em></strong></dt> <dd> <p>Specify whether to modify HEADER record during the generation of new PDB files Possible values: <em>yes | no</em>. Default: <em>yes</em>. By defailt, Classification data is replaced by <em>Data modified using MayaChemTools</em> before writing out HEADER record.</p> </dd> <dt><strong><strong>-o, --overwrite</strong></strong></dt> <dd> <p>Overwrite existing files</p> </dd> <dt><strong><strong>--ResidueNumberMode</strong> <em>Sequential | PerChain</em></strong></dt> <dd> <p>Specify how to renumber residues: renumber residues sequentially across all the chains or start from the begining for each chain. Possible values: <em>Sequential | PerChain</em>. Default: <em>PerChain</em>.</p> </dd> <dt><strong><strong>--ResidueNumberStart</strong> <em>number</em></strong></dt> <dd> <p>Starting residue number to use for ATOM records in chains. Default: <em>1</em>. Valid values positive integers.</p> <p>For <em>Sequential</em> value of <strong>--ResidueNumberMode</strong> option, residue numbers are assigned sequentially across all the chains starting from the specified value.</p> <p>For <em>PerChain</em> value of <strong>--ResidueNumberMode</strong> option, residue numbers are starting again from the specified value for each chain.</p> <p>HETATM residues with in the chains are numbered using this value as well</p> </dd> <dt><strong><strong>--ResidueNumberHetatmMode</strong> <em>automatic | specify</em></strong></dt> <dd> <p>Specify how to start residue number for HETATM records: use the next sequential residue number after the last residue number from ATOM records or start from a specific residue number. Possible values: <em>automatic | specify</em>. Default: <em>automatic</em></p> <p>For <em>automatic</em> , residue number after highest residue number of ATOM records is used as the starting residue number for HETATM records.</p> <p>For <em>specify</em>, value of option <strong>--ResidueNumberStarHetatm</strong> is used as the starting residue number for HETATM records.</p> <p>This option along with <strong>--ResidueNumberStartHetatm</strong> only applies to HETATM records outside the chains.</p> </dd> <dt><strong><strong>--ResidueNumberStartHetatm</strong> <em>number</em></strong></dt> <dd> <p>Starting residue number to use for HETATM records. Default: <em>6000</em>. Valid values positive integers.</p> </dd> <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> <dd> <p>New PDB and sequence file name is generated using the root: <Root><Mode>.<Ext>. Default new file name: <PDBFileName><Mode>.pdb. This option is ignored for multiple input files.</p> </dd> <dt><strong><strong>--WaterResidueNames</strong> <em>Automatic | "ResidueName,[ResidueName,...]"</em></strong></dt> <dd> <p>Identification of water residues during <em>RenumberWaters</em> value of <strong>-m, --mode</strong> option. Possible values: <em>Automatic | "ResidueName,[ResidueName,...]"</em>. Default: <em>Automatic</em> which corresponds to "HOH,WAT,H20". You can also specify a different comma delimited list of residue names to use for water.</p> </dd> <dt><strong><strong>--WaterResidueStart</strong> <em>number</em></strong></dt> <dd> <p>Starting water residue number to use during <em>RenumberWaters</em> <strong>-m, --mode</strong> value. Default: <em>8000</em>. Valid values: positive integers.</p> </dd> <dt><strong><strong>-w, --WorkingDir</strong> <em>dirname</em></strong></dt> <dd> <p>Location of working directory. Default: current directory.</p> </dd> </dl> <p> </p> <h2>EXAMPLES</h2> <p>To renumber ATOM and HETATM residues starting from 1 for each chain with continuation to HETATM residues outside TER records in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type:</p> <div class="ExampleBox"> % ModifyPDBFiles.pl Sample1.pdb</div> <p>To renumber ATOM and HETATM residues sequentially across all chains starting from 1 with continuation to HETATM residues outside TER records in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type:</p> <div class="ExampleBox"> % ModifyPDBFiles.pl --ResidueNumberMode Sequential -o Sample1.pdb</div> <p>To renumber ATOM and HETATM residues sequentially across all chains starting from 1 and HETATM residues outside TER records starting from 6000 in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type:</p> <div class="ExampleBox"> % ModifyPDBFiles.pl --ResidueNumberMode Sequential --ResidueNumberHetatmMode Specify -o Sample1.pdb</div> <p>To renumber ATOM and HETATM residues sequentially across all chains starting from 100 for ATOM/HETATM residues with in TER records and starting from 999 for HETATM residues outside TER records in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type:</p> <div class="ExampleBox"> % ModifyPDBFiles.pl --ResidueNumberMode Sequential --ResidueNumberHetatmMode Specify --ResidueNumberStart 100 --ResidueNumberStartHetatm 999 -o Sample2.pdb</div> <p>To renumber ATOM and HETATM residues from 100 for each chain and starting from 999 for HETATM residues outside TER records in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type:</p> <div class="ExampleBox"> % ModifyPDBFiles.pl --ResidueNumberMode PerChain --ResidueNumberHetatmMode Specify --ResidueNumberStart 100 --ResidueNumberStartHetatm 999 -o Sample2.pdb</div> <p>To renumber ATOM serial numbers sequentially starting from 100 in Sample1.pdb file and generate Sample1RenumberAtoms.pdb file, type:</p> <div class="ExampleBox"> % ModifyPDBFiles.pl -m RenumberAtoms --AtomNumberStart 100 -o Sample1.pdb</div> <p>To renumber water residues identified by "HOH,WAT" starting from residue number 1000 in Sample2.pdb file and generate Sample2RenumberWaters.pdb file, type:</p> <div class="ExampleBox"> % ModifyPDBFiles.pl -m RenumberWaters --WaterResidueNames "HOH,WAT" -o --WaterResidueStart 950 Sample2.pdb</div> <p>To rename all chain IDs starting from A in Sample1.pdb file and generate Sample1RenameChainIDs.pdb file, type:</p> <div class="ExampleBox"> % ModifyPDBFiles.pl -m RenameChainIDs -o Sample1.pdb</div> <p>To rename all chain IDs starting from B without assigning any chain IDs to ATOM/HETATOM with no chain IDs in Sample2.pdb file and generate Sample2RenameChainIDs.pdb file, type:</p> <div class="ExampleBox"> % ModifyPDBFiles.pl l -m RenameChainIDs -c B --ChainIDRenameEmpty No -o Sample2.pdb</div> <p> </p> <h2>AUTHOR</h2> <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> <p> </p> <h2>SEE ALSO</h2> <p><a href="./ExtractFromPDBFiles.html">ExtractFromPDBFiles.pl</a>, <a href="./InfoPDBFiles.html">InfoPDBFiles.pl</a> </p> <p> </p> <h2>COPYRIGHT</h2> <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> <p>This file is part of MayaChemTools.</p> <p>MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.</p> <p> </p><p> </p><div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <tr align="left" valign="top"><td width="33%" align="left"><a href="./ModifyNewLineChar.html" title="ModifyNewLineChar.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ModifySDFilesDataFields.html" title="ModifySDFilesDataFields.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ModifyPDBFiles.pl</strong></td></tr> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>