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3 <title>MayaChemTools:Documentation:ModifyPDBFiles.pl</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ModifyNewLineChar.html" title="ModifyNewLineChar.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>&nbsp;|&nbsp;<a href="./../pdf/ModifyPDBFiles.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/ModifyPDBFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/ModifyPDBFiles.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/ModifyPDBFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>ModifyPDBFiles.pl - Modify data in PDBFile(s)</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>ModifyPDBFiles.pl PDBFile(s)...</p>
26 <p>ModifyPDBFiles.pl [<strong>-a, --AtomNumberStart</strong> number] [<strong>-c, --ChainIDStart</strong> character]
27 [<strong>--ChainIDRenameEmpty</strong> yes | no] [<strong>-h, --help</strong>] [<strong>-k, --KeepOldRecords</strong> yes | no]
28 [<strong>-m, --mode </strong> RenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs]
29 [<strong>--ModifyHeader</strong> yes | no] [<strong>-o, --overwrite</strong>] [<strong>--ResidueNumberMode</strong> Sequential | PerChain]
30 [<strong>--ResidueNumberStart</strong> number] [<strong>--ResidueNumberHetatmMode</strong> automatic | specify]
31 [<strong>--ResidueNumberStarHetatm</strong> number] [<strong>-r, --root</strong> rootname]
32 [<strong>--WaterResidueNames</strong> Automatic | &quot;ResidueName, [ResidueName,...]&quot;] [<strong>--WaterResidueStart</strong> number]
33 [<strong>-w, --WorkingDir</strong> dirname] PDBFile(s)...</p>
34 <p>
35 </p>
36 <h2>DESCRIPTION</h2>
37 <p>Modify data in <em>PDBFile(s)</em>: renumber atoms, residues, and water residues or assign new
38 chain IDs. Multiple PDBFile names are separated by spaces. The valid file extension is <em>.pdb</em>.
39 All other file name extensions are ignored during the wild card expansion. All the PDB files
40 in a current directory can be specified either by <em>*.pdb</em> or the current directory name.</p>
41 <p>
42 </p>
43 <h2>OPTIONS</h2>
44 <dl>
45 <dt><strong><strong>-a, --AtomNumberStart</strong> <em>number</em></strong></dt>
46 <dd>
47 <p>Starting atom number to use during <em>RenumberAtoms</em> value of <strong>-m, --mode</strong> option. Default: <em>1</em>.
48 Valid values: positive integers.</p>
49 </dd>
50 <dt><strong><strong>-c, --ChainIDStart</strong> <em>character</em></strong></dt>
51 <dd>
52 <p>A single character to use for starting IDs for chains during <em>RenameChainIDs</em> value of <strong>-m, --mode</strong> option.
53 Default: <em>A</em>. Valid values: <em>A to Z</em>.</p>
54 </dd>
55 <dt><strong><strong>--ChainIDRenameEmpty</strong> <em>Yes | No</em></strong></dt>
56 <dd>
57 <p>Specify whether to rename empty chain IDs during <em>RenameChainIDs</em> <strong>-m, --mode</strong> value. By
58 default, ATOM and HETATM records with no chain IDs are left unchanged. Possible values:
59 <em>yes | no</em>. Default: <em>No</em>.</p>
60 </dd>
61 <dt><strong><strong>-h, --help</strong></strong></dt>
62 <dd>
63 <p>Print this help message.</p>
64 </dd>
65 <dt><strong><strong>-k, --KeepOldRecords</strong> <em>yes | no</em></strong></dt>
66 <dd>
67 <p>Specify whether to transfer old non ATOM and HETATM records from input PDBFile(s) to new
68 PDBFile(s). By default, except for the HEADER record, all records other than ATOM/HETATM
69 are dropped during the generation of new PDB files. Possible values: <em>yes | no</em>.
70 Default: <em>no</em>.</p>
71 </dd>
72 <dt><strong><strong>-m, --mode </strong> <em>RenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs</em></strong></dt>
73 <dd>
74 <p>Specify how to modify <em>PDBFile(s)</em>. Possible values: <em>RenumberAtoms | RenumberResidues
75 | RenumberWaters | RenameChainIDs</em>. Default: <em>RenumberResidues</em>.</p>
76 <p>For <em>RenumberAtoms</em> mode, residue number in ATOM and HETATM records are reassigned
77 sequentially starting using value of <strong>-a, --AtomNumberStart</strong> option.</p>
78 <p>For <em>RenumberResidues</em> mode, serial number in ATOM and HETATM records are reassigned
79 either sequentially or statring from specified values for ATOM and HETATM records in each
80 chain.</p>
81 <p>For <em>RenumberWaters</em> mode, residue number for waters are reassigned starting from a specific
82 value.</p>
83 <p>For <em>RenameChainIDs</em> mode, all the chain IDs are reassigned starting from a specific chain ID.</p>
84 <p>During the generation of new PDB files, unnecessary CONECT records are dropped.</p>
85 </dd>
86 <dt><strong><strong>--ModifyHeader</strong> <em>yes | no</em></strong></dt>
87 <dd>
88 <p>Specify whether to modify HEADER record during the generation of new PDB files
89 Possible values: <em>yes | no</em>. Default: <em>yes</em>. By defailt, Classification data is replaced
90 by <em>Data modified using MayaChemTools</em> before writing out HEADER record.</p>
91 </dd>
92 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
93 <dd>
94 <p>Overwrite existing files</p>
95 </dd>
96 <dt><strong><strong>--ResidueNumberMode</strong> <em>Sequential | PerChain</em></strong></dt>
97 <dd>
98 <p>Specify how to renumber residues: renumber residues sequentially across all the chains
99 or start from the begining for each chain. Possible values: <em>Sequential | PerChain</em>. Default:
100 <em>PerChain</em>.</p>
101 </dd>
102 <dt><strong><strong>--ResidueNumberStart</strong> <em>number</em></strong></dt>
103 <dd>
104 <p>Starting residue number to use for ATOM records in chains. Default: <em>1</em>. Valid values
105 positive integers.</p>
106 <p>For <em>Sequential</em> value of <strong>--ResidueNumberMode</strong> option, residue numbers are
107 assigned sequentially across all the chains starting from the specified value.</p>
108 <p>For <em>PerChain</em> value of <strong>--ResidueNumberMode</strong> option, residue numbers are
109 starting again from the specified value for each chain.</p>
110 <p>HETATM residues with in the chains are numbered using this value as well</p>
111 </dd>
112 <dt><strong><strong>--ResidueNumberHetatmMode</strong> <em>automatic | specify</em></strong></dt>
113 <dd>
114 <p>Specify how to start residue number for HETATM records: use the next sequential
115 residue number after the last residue number from ATOM records or start from a
116 specific residue number. Possible values: <em>automatic | specify</em>. Default:
117 <em>automatic</em></p>
118 <p>For <em>automatic</em> , residue number after highest residue number of ATOM
119 records is used as the starting residue number for HETATM records.</p>
120 <p>For <em>specify</em>, value of option <strong>--ResidueNumberStarHetatm</strong> is used as the
121 starting residue number for HETATM records.</p>
122 <p>This option along with <strong>--ResidueNumberStartHetatm</strong> only applies to HETATM records
123 outside the chains.</p>
124 </dd>
125 <dt><strong><strong>--ResidueNumberStartHetatm</strong> <em>number</em></strong></dt>
126 <dd>
127 <p>Starting residue number to use for HETATM records. Default: <em>6000</em>. Valid values
128 positive integers.</p>
129 </dd>
130 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
131 <dd>
132 <p>New PDB and sequence file name is generated using the root: &lt;Root&gt;&lt;Mode&gt;.&lt;Ext&gt;.
133 Default new file name: &lt;PDBFileName&gt;&lt;Mode&gt;.pdb. This option is ignored for multiple
134 input files.</p>
135 </dd>
136 <dt><strong><strong>--WaterResidueNames</strong> <em>Automatic | &quot;ResidueName,[ResidueName,...]&quot;</em></strong></dt>
137 <dd>
138 <p>Identification of water residues during <em>RenumberWaters</em> value of <strong>-m, --mode</strong> option. Possible
139 values: <em>Automatic | &quot;ResidueName,[ResidueName,...]&quot;</em>. Default: <em>Automatic</em> which corresponds
140 to &quot;HOH,WAT,H20&quot;. You can also specify a different comma delimited list of residue names
141 to use for water.</p>
142 </dd>
143 <dt><strong><strong>--WaterResidueStart</strong> <em>number</em></strong></dt>
144 <dd>
145 <p>Starting water residue number to use during <em>RenumberWaters</em> <strong>-m, --mode</strong> value.
146 Default: <em>8000</em>. Valid values: positive integers.</p>
147 </dd>
148 <dt><strong><strong>-w, --WorkingDir</strong> <em>dirname</em></strong></dt>
149 <dd>
150 <p>Location of working directory. Default: current directory.</p>
151 </dd>
152 </dl>
153 <p>
154 </p>
155 <h2>EXAMPLES</h2>
156 <p>To renumber ATOM and HETATM residues starting from 1 for each chain with continuation to
157 HETATM residues outside TER records in Sample2.pdb and generate
158 Sample2RenumberResidues.pdb file, type:</p>
159 <div class="ExampleBox">
160 % ModifyPDBFiles.pl Sample1.pdb</div>
161 <p>To renumber ATOM and HETATM residues sequentially across all chains starting from 1 with
162 continuation to HETATM residues outside TER records in Sample2.pdb and generate
163 Sample2RenumberResidues.pdb file, type:</p>
164 <div class="ExampleBox">
165 % ModifyPDBFiles.pl --ResidueNumberMode Sequential -o Sample1.pdb</div>
166 <p>To renumber ATOM and HETATM residues sequentially across all chains starting from 1 and
167 HETATM residues outside TER records starting from 6000 in Sample2.pdb and generate
168 Sample2RenumberResidues.pdb file, type:</p>
169 <div class="ExampleBox">
170 % ModifyPDBFiles.pl --ResidueNumberMode Sequential
171 --ResidueNumberHetatmMode Specify -o Sample1.pdb</div>
172 <p>To renumber ATOM and HETATM residues sequentially across all chains starting from 100 for
173 ATOM/HETATM residues with in TER records and starting from 999 for HETATM residues
174 outside TER records in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type:</p>
175 <div class="ExampleBox">
176 % ModifyPDBFiles.pl --ResidueNumberMode Sequential
177 --ResidueNumberHetatmMode Specify --ResidueNumberStart 100
178 --ResidueNumberStartHetatm 999 -o Sample2.pdb</div>
179 <p>To renumber ATOM and HETATM residues from 100 for each chain and starting from 999 for
180 HETATM residues outside TER records in Sample2.pdb and generate Sample2RenumberResidues.pdb
181 file, type:</p>
182 <div class="ExampleBox">
183 % ModifyPDBFiles.pl --ResidueNumberMode PerChain
184 --ResidueNumberHetatmMode Specify --ResidueNumberStart 100
185 --ResidueNumberStartHetatm 999 -o Sample2.pdb</div>
186 <p>To renumber ATOM serial numbers sequentially starting from 100 in Sample1.pdb file and generate
187 Sample1RenumberAtoms.pdb file, type:</p>
188 <div class="ExampleBox">
189 % ModifyPDBFiles.pl -m RenumberAtoms --AtomNumberStart 100
190 -o Sample1.pdb</div>
191 <p>To renumber water residues identified by &quot;HOH,WAT&quot; starting from residue number 1000
192 in Sample2.pdb file and generate Sample2RenumberWaters.pdb file, type:</p>
193 <div class="ExampleBox">
194 % ModifyPDBFiles.pl -m RenumberWaters --WaterResidueNames &quot;HOH,WAT&quot;
195 -o --WaterResidueStart 950 Sample2.pdb</div>
196 <p>To rename all chain IDs starting from A in Sample1.pdb file and generate
197 Sample1RenameChainIDs.pdb file, type:</p>
198 <div class="ExampleBox">
199 % ModifyPDBFiles.pl -m RenameChainIDs -o Sample1.pdb</div>
200 <p>To rename all chain IDs starting from B without assigning any chain IDs to ATOM/HETATOM
201 with no chain IDs in Sample2.pdb file and generate Sample2RenameChainIDs.pdb file, type:</p>
202 <div class="ExampleBox">
203 % ModifyPDBFiles.pl l -m RenameChainIDs -c B --ChainIDRenameEmpty No
204 -o Sample2.pdb</div>
205 <p>
206 </p>
207 <h2>AUTHOR</h2>
208 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
209 <p>
210 </p>
211 <h2>SEE ALSO</h2>
212 <p><a href="./ExtractFromPDBFiles.html">ExtractFromPDBFiles.pl</a>,&nbsp<a href="./InfoPDBFiles.html">InfoPDBFiles.pl</a>
213 </p>
214 <p>
215 </p>
216 <h2>COPYRIGHT</h2>
217 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
218 <p>This file is part of MayaChemTools.</p>
219 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
220 the terms of the GNU Lesser General Public License as published by the Free
221 Software Foundation; either version 3 of the License, or (at your option)
222 any later version.</p>
223 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
224 <table width="100%" border=0 cellpadding=0 cellspacing=2>
225 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ModifyNewLineChar.html" title="ModifyNewLineChar.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>
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