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1 <html>
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3 <title>MayaChemTools:Documentation:InfoPDBFiles.pl</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./InfoNucleicAcids.html" title="InfoNucleicAcids.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./InfoPeriodicTableElements.html" title="InfoPeriodicTableElements.html">Next</a></td><td width="34%" align="middle"><strong>InfoPDBFiles.pl</strong></td><td width="33%" align="right"><a href="././code/InfoPDBFiles.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/InfoPDBFiles.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/InfoPDBFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/InfoPDBFiles.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/InfoPDBFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
16 </table>
17 </div>
18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>InfoPDBFiles.pl - List information about PDB files</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>InfoPDBFiles.pl PDBFile(s) PDB(s)...</p>
26 <p>InfoPDBFiles.pl [<strong>-a, --all</strong>] [<strong>-b, --BoundingBox</strong>]
27 [<strong>-c, --count</strong> &quot;RecordType, [RecordType,...]&quot; | All] [<strong>--chains</strong>]
28 [<strong>-d, --detail</strong> infolevel] [<strong>-e, --experiment</strong>] [<strong>-f, --frequency</strong>]
29 [<strong>-h, --help</strong>] [<strong>--header</strong>] [<strong>m, --MasterCheck</strong>] [<strong>--residues</strong>]
30 [<strong>--ResiduesMode</strong> InChains | All | Both] [<strong>--ResidueNumbers</strong>]
31 [<strong>-w, --WorkingDir</strong> dirname] PDBFile(s)...</p>
32 <p>
33 </p>
34 <h2>DESCRIPTION</h2>
35 <p>List information about contents of <em>PDBFile(s)</em>: number of each record type, number of chains,
36 count and percent distribution of residues in each chain, bounding box and so on.
37 Multiple PDBFile names are separated by spaces. The valid file extension is <em>.pdb</em>.
38 All other file name extensions are ignored during the wild card expansion. All the PDB files
39 in a current directory can be specified either by <em>*.pdb</em> or the current directory name.</p>
40 <p>In PDB files containing data for multiple models, all ATOM/HETAM records for chains after the first model
41 are ignored.</p>
42 <p>
43 </p>
44 <h2>OPTIONS</h2>
45 <dl>
46 <dt><strong><strong>-a, --all</strong></strong></dt>
47 <dd>
48 <p>List all the available information.</p>
49 </dd>
50 <dt><strong><strong>-b, --BoundingBox</strong></strong></dt>
51 <dd>
52 <p>List min/max XYZ coordiates of ATOM/HETATM records.</p>
53 </dd>
54 <dt><strong><strong>-c, --count</strong> <em>RecordType,[RecordType,...]|All</em></strong></dt>
55 <dd>
56 <p>Types of PDB records to count in <em>PDBFile(s)</em>. You can specify a list of any valid PDB
57 record type or count all record types found in the files. Possible values: Comma delimited list
58 of valid <em>RecordTypes</em> or <em>All</em>. Default: <em>ATOM,HETATM</em>. And this is also <strong>default behavior</strong>.</p>
59 <p>The list of valid PDB record types includes: <em>HEADER, OBSLTE, TITLE, CAVEAT, COMPND, SOURCE, KEYWDS,
60 EXPDTA, AUTHOR, REVDAT, SPRSDE, JRN, REMARK, DBRE, SEQADV, SEQRES, MODRES, HET, HETNAM, HETSYN,
61 FORMUL, HELIX, SHEET, TURN, SSBOND, LINK, HYDBND, SLTBRG, CISPEP, SITE, CRYST1, ORIGX1, ORIGX2, ORIGX3,
62 SCALE1, SCALE2, SCALE3, MTRIX1 MTRIX2 MTRIX3, TVECT, MODEL, ATOM, SIGATM, ANISOU, SIGUIJ, TER,
63 HETATM, ENDMDL, CONECT, MASTER, END</em>.</p>
64 </dd>
65 <dt><strong><strong>--chains</strong></strong></dt>
66 <dd>
67 <p>Count number of chains.</p>
68 </dd>
69 <dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt>
70 <dd>
71 <p>Level of information to print about PDB during various options. Default: <em>1</em>.
72 Possible values: <em>1, 2 or 3</em>.</p>
73 </dd>
74 <dt><strong><strong>-e, --experiment</strong></strong></dt>
75 <dd>
76 <p>List experimental technique information along with any applicable resolution.</p>
77 </dd>
78 <dt><strong><strong>-f, --frequency</strong></strong></dt>
79 <dd>
80 <p>List distribution of residues: report count and percent of residues in individual chains and
81 across all the chains, or for all the residues in the file. The value of option <strong>--residuesmode</strong>
82 determines how residues are counted and what is listed. The list is sorted by frequency in
83 descending order. By default, only residue count values are reported. To list percent distribution
84 of residues, specify <strong>-d, --detail</strong> value of <em>2</em> or higher.</p>
85 </dd>
86 <dt><strong><strong>-h, --help</strong></strong></dt>
87 <dd>
88 <p>Print this help message.</p>
89 </dd>
90 <dt><strong><strong>--header</strong></strong></dt>
91 <dd>
92 <p>List header information.</p>
93 </dd>
94 <dt><strong><strong>m, --MasterCheck</strong></strong></dt>
95 <dd>
96 <p>Check master record by explicitly counting the number of REMARK, HET, HELIX, SHEET, TURN, SITE,
97 ORIGX, SCALE, MTRIX, ATOM, HETATM, TER, CONECT and SEQRES records and comparing their
98 values against contents of master record.</p>
99 </dd>
100 <dt><strong><strong>--residues</strong></strong></dt>
101 <dd>
102 <p>Count residues in <em>PDBFile(s)</em>. This is also <strong>default behavior</strong>.</p>
103 <p>By default, only residue count values are reported. To list percent distribution of residues,
104 specify <strong>-d, --detail</strong> value of <em>2</em> or higher.</p>
105 </dd>
106 <dt><strong><strong>--ResiduesMode</strong> &lt;InChains | All | Both&gt;</strong></dt>
107 <dd>
108 <p>Specify how to count residues in <em>PDBFile(s)</em>: Count residue in each chain and across all the chains,
109 list count iof all the residues in the file, or list both. Possible values: <em>InChains, All, or Both</em>.
110 Default: <em>Both</em>.</p>
111 </dd>
112 <dt><strong><strong>--ResidueNumbers</strong></strong></dt>
113 <dd>
114 <p>List information about ATOM residue numbers in each chain before TER record: start and end residue
115 number; gaps in residue numbers corresponding to non-sequential residue numbers; residue
116 numbers not in ascending order.</p>
117 </dd>
118 <dt><strong><strong>-w, --WorkingDir</strong> <em>dirname</em></strong></dt>
119 <dd>
120 <p>Location of working directory. Default: current directory.</p>
121 </dd>
122 </dl>
123 <p>
124 </p>
125 <h2>EXAMPLES</h2>
126 <p>To list total number of records and number of chain(s) residues in PDB files, type:</p>
127 <div class="ExampleBox">
128 % InfoPDBFiles.pl Sample1.pdb
129 <br/>% InfoPDBFiles.pl Sample2.pdb</div>
130 <p>To list all available information for PDB file Sample2.pdb, type:</p>
131 <div class="ExampleBox">
132 % InfoPDBFiles.pl -a Sample2.pdb</div>
133 <p>To list all available information for PDB file Sample2.pdb with all available details, type:</p>
134 <div class="ExampleBox">
135 % InfoPDBFiles.pl -a -d Sample2.pdb</div>
136 <p>To count ATOM and HETATM records in Sample2.pdb file, type:</p>
137 <div class="ExampleBox">
138 % InfoPDBFiles.pl -c &quot;ATOM,HETATM&quot; Sample2.pdb</div>
139 <p>To list distribution of residues in chains across the whole PDB file Sample2.pdb along with
140 percent distribution, type</p>
141 <div class="ExampleBox">
142 % InfoPDBFiles.pl --frequency -d 2 Sample2.pdb</div>
143 <p>To list distribution of residues only across chains in PDB file Sample2.pdb along with
144 percent distribution, type</p>
145 <div class="ExampleBox">
146 % InfoPDBFiles.pl --frequency -d 2 --ResiduesMode InChains Sample2.pdb</div>
147 <p>To list min/max coordinates of the bounding box which encompasses the structure in Sample1.pdb
148 file, type:</p>
149 <div class="ExampleBox">
150 % InfoPDBFiles.pl -b Sample1.pdb</div>
151 <p>
152 </p>
153 <h2>AUTHOR</h2>
154 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
155 <p>
156 </p>
157 <h2>SEE ALSO</h2>
158 <p><a href="./ExtractFromPDBFiles.html">ExtractFromPDBFiles.pl</a>,&nbsp<a href="./InfoAminoAcids.html">InfoAminoAcids.pl</a>,&nbsp<a href="./InfoNucleicAcids.html">InfoNucleicAcids.pl</a>,&nbsp<a href="./InfoSequenceFiles.html">InfoSequenceFiles.pl</a>,&nbsp<a href="./ModifyPDBFiles.html">ModifyPDBFiles.pl</a>
159 </p>
160 <p>
161 </p>
162 <h2>COPYRIGHT</h2>
163 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
164 <p>This file is part of MayaChemTools.</p>
165 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
166 the terms of the GNU Lesser General Public License as published by the Free
167 Software Foundation; either version 3 of the License, or (at your option)
168 any later version.</p>
169 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
170 <table width="100%" border=0 cellpadding=0 cellspacing=2>
171 <tr align="left" valign="top"><td width="33%" align="left"><a href="./InfoNucleicAcids.html" title="InfoNucleicAcids.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./InfoPeriodicTableElements.html" title="InfoPeriodicTableElements.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>InfoPDBFiles.pl</strong></td></tr>
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