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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./ExtractFromSDFiles.html" title="ExtractFromSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>ExtractFromPDBFiles.pl</strong></td><td width="33%" align="right"><a href="././code/ExtractFromPDBFiles.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/ExtractFromPDBFiles.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/ExtractFromPDBFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/ExtractFromPDBFiles.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/ExtractFromPDBFiles.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>ExtractFromPDBFiles.pl - Extract specific data from PDBFile(s)</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>ExtractFromPDBFiles.pl PDBFile(s)...</p>
26 <p>ExtractFromPDBFiles.pl [<strong>-a, --Atoms</strong> &quot;AtomNum, [AtomNum...]&quot; | &quot;StartAtomNum, EndAtomNum&quot; |
27 &quot;AtomName, [AtomName...]&quot;] [<strong>-c, --chains</strong> First | All | &quot;ChainID, [ChainID,...]&quot;]
28 [&lt;--CombineChains&gt; yes | no] [<strong>-d, --distance</strong> number] [<strong>--DistanceMode</strong> Atom | Hetatm | Residue | XYZ]
29 [<strong>--DistanceOrigin</strong> &quot;AtomNumber, AtomName&quot; | &quot;HetatmNumber, HetAtmName&quot; | &quot;ResidueNumber, ResidueName, [ChainID]&quot; | &quot;X,Y,Z&quot;&gt;]
30 [&lt;--DistanceSelectionMode&gt; ByAtom | ByResidue] [<strong>-h, --help</strong>] [<strong>-k, --KeepOldRecords</strong> yes | no]
31 [<strong>-m, --mode </strong> Chains | Sequences | Atoms | CAlphas | AtomNums | AtomsRange | AtomNames |
32 ResidueNums | ResiduesRange | ResidueNames | Distance | NonWater | NonHydrogens]
33 [<strong>--ModifyHeader</strong> yes | no] [<strong>--NonStandardKeep</strong> yes | no] [<strong>--NonStandardCode</strong> character]
34 [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname] <strong>--RecordMode</strong> <em>Atom | Hetatm | AtomAndHetatm</em>]
35 [<strong>--Residues</strong> &quot;ResidueNum,[ResidueNum...]&quot; | StartResidueNum,EndResiduNum ]
36 [<strong>--SequenceLength</strong> number] [<strong>--SequenceRecords</strong> Atom | SeqRes]
37 [<strong>--SequenceIDPrefix</strong> FileName | HeaderRecord | Automatic]
38 [<strong>--WaterResidueNames</strong> Automatic | &quot;ResidueName, [ResidueName,...]&quot;]
39 [<strong>-w, --WorkingDir</strong> dirname] PDBFile(s)...</p>
40 <p>
41 </p>
42 <h2>DESCRIPTION</h2>
43 <p>Extract specific data from <em>PDBFile(s)</em> and generate appropriate PDB or sequence file(s).
44 Multiple PDBFile names are separated by spaces. The valid file extension is <em>.pdb</em>.
45 All other file name extensions are ignored during the wild card expansion. All the PDB files
46 in a current directory can be specified either by <em>*.pdb</em> or the current directory name.</p>
47 <p>During <em>Chains</em> and <em>Sequences</em> values of <strong>-m, --mode</strong> option, all ATOM/HETAM records
48 for chains after the first model in PDB fils containing data for multiple models are ignored.</p>
49 <p>
50 </p>
51 <h2>OPTIONS</h2>
52 <dl>
53 <dt><strong><strong>-a, --Atoms</strong> <em>&quot;AtomNum,[AtomNum...]&quot; | &quot;StartAtomNum,EndAtomNum&quot; | &quot;AtomName,[AtomName...]&quot;</em></strong></dt>
54 <dd>
55 <p>Specify which atom records to extract from <em>PDBFiles(s)</em> during <em>AtomNums</em>,
56 <em>AtomsRange</em>, and <em>AtomNames</em> value of <strong>-m, --mode</strong> option: extract records
57 corresponding to atom numbers specified in a comma delimited list of atom numbers/names,
58 or with in the range of start and end atom numbers. Possible values: <em>&quot;AtomNum[,AtomNum,..]&quot;</em>,
59 <em>StartAtomNum,EndAtomNum</em>, or <em>&quot;AtomName[,AtomName,..]&quot;</em>. Default: <em>None</em>. Examples:</p>
60 <div class="OptionsBox">
61 10
62 <br/> 15,20
63 <br/> N,CA,C,O</div>
64 </dd>
65 <dt><strong><strong>-c, --chains</strong> <em>First | All | ChainID,[ChainID,...]</em></strong></dt>
66 <dd>
67 <p>Specify which chains to extract from <em>PDBFile(s)</em> during <em>Chains | Sequences</em> value of
68 <strong>-m, --mode</strong> option: first chain, all chains, or a specific list of comma delimited chain IDs.
69 Possible values: <em>First | All | ChainID,[ChainID,...]</em>. Default: <em>First</em>. Examples:</p>
70 <div class="OptionsBox">
71 A
72 <br/> A,B
73 <br/> All</div>
74 </dd>
75 <dt><strong><strong>--CombineChains</strong> <em>yes | no</em></strong></dt>
76 <dd>
77 <p>Specify whether to combine extracted chains data into a single file during <em>Chains</em> or
78 <em>Sequences</em> value of <strong>-m, --mode</strong> option. Possible values: <em>yes | no</em>. Default: <em>no</em>.</p>
79 <p>During <em>Chains</em> value of &lt;-m, --mode&gt; option with <em>Yes</em> value of &lt;--CombineChains&gt;,
80 extracted data for specified chains is written into a single file instead of individual file for each
81 chain.</p>
82 <p>During <em>Sequences</em> value of &lt;-m, --mode&gt; option with <em>Yes</em> value of &lt;--CombineChains&gt;,
83 residues sequences for specified chains are extracted and concatenated into a single sequence
84 file instead of individual file for each chain.</p>
85 </dd>
86 <dt><strong><strong>-d, --distance</strong> <em>number</em></strong></dt>
87 <dd>
88 <p>Specify distance used to extract ATOM/HETATM recods during <em>Distance</em> value of
89 <strong>-m, --mode</strong> option. Default: <em>10.0</em> angstroms.</p>
90 <p><strong>--RecordMode</strong> option controls type of record lines to extract from <em>PDBFile(s)</em>:
91 ATOM, HETATM or both.</p>
92 </dd>
93 <dt><strong><strong>--DistanceMode</strong> <em>Atom | Hetatm | Residue | XYZ</em></strong></dt>
94 <dd>
95 <p>Specify how to extract ATOM/HETATM records from <em>PDBFile(s)</em> during <em>Distance</em> value of
96 <strong>-m, --mode</strong> option: extract all the records within a certain distance specifed by <strong>-d, --distance</strong>
97 from an atom or hetro atom record, a residue, or any artbitrary point. Possible values: <em>Atom |
98 Hetatm | Residue | XYZ</em>. Default: <em>XYZ</em>.</p>
99 <p>During <em>Residue</em> value of <strong>--distancemode</strong>, distance of ATOM/HETATM records is calculated from
100 all the atoms in the residue and the records are selected as long as any atom of the residue lies with
101 in the distace specified using <strong>-d, --distance</strong> option.</p>
102 <p><strong>--RecordMode</strong> option controls type of record lines to extract from <em>PDBFile(s)</em>:
103 ATOM, HETATM or both.</p>
104 </dd>
105 <dt><strong><strong>--DistanceSelectionMode</strong> <em>ByAtom | ByResidue</em></strong></dt>
106 <dd>
107 <p>Specify how how to extract ATOM/HETATM records from <em>PDBFile(s)</em> during <em>Distance</em> value of
108 <strong>-m, --mode</strong> option for all values of <strong>--DistanceMode</strong> option: extract only those ATOM/HETATM
109 records that meet specified distance criterion; extract all records corresponding to a residue as
110 long as one of the ATOM/HETATM record in the residue satisfies specified distance criterion. Possible
111 values: <em>ByAtom, ByResidue</em>. Default value: <em>ByAtom</em>.</p>
112 </dd>
113 <dt><strong><strong>--DistanceOrigin</strong> <em>&quot;AtomNumber,AtomName&quot; | &quot;HetatmNumber,HetAtmName&quot; | &quot;ResidueNumber,ResidueName[,ChainID]&quot; | &quot;X,Y,Z&quot;</em></strong></dt>
114 <dd>
115 <p>This value is <strong>--distancemode</strong> specific. In general, it identifies a point used to select
116 other ATOM/HETATMS with in a specific distance from this point.</p>
117 <p>For <em>Atom</em> value of <strong>--distancemode</strong>, this option corresponds to an atom specification.
118 Format: <em>AtomNumber,AtomName</em>. Example:</p>
119 <div class="OptionsBox">
120 455,CA</div>
121 <p>For <em>Hetatm</em> value of <strong>--distancemode</strong>, this option corresponds to a hetatm specification.
122 Format: <em>HetatmNumber,HetAtmName</em>. Example:</p>
123 <div class="OptionsBox">
124 5295,C1</div>
125 <p>For <em>Residue</em> value of <strong>--distancemode</strong>, this option corresponds to a residue specification.
126 Format: <em>ResidueNumber, ResidueName[,ChainID]</em>. Example:</p>
127 <div class="OptionsBox">
128 78,MSE
129 <br/> 977,RET,A
130 <br/> 978,RET,B</div>
131 <p>For <em>XYZ</em> value of <strong>--distancemode</strong>, this option corresponds to a coordinate of an
132 arbitrary point. Format: <em>X,Y,X</em>. Example:</p>
133 <div class="OptionsBox">
134 10.044,19.261,-4.292</div>
135 <p><strong>--RecordMode</strong> option controls type of record lines to extract from <em>PDBFile(s)</em>:
136 ATOM, HETATM or both.</p>
137 </dd>
138 <dt><strong><strong>-h, --help</strong></strong></dt>
139 <dd>
140 <p>Print this help message.</p>
141 </dd>
142 <dt><strong><strong>-k, --KeepOldRecords</strong> <em>yes | no</em></strong></dt>
143 <dd>
144 <p>Specify whether to transfer old non ATOM and HETATM records from input PDBFile(s) to new
145 PDBFile(s) during <em>Chains | Atoms | HetAtms | CAlphas | Distance| NonWater | NonHydrogens</em>
146 value of <strong>-m --mode</strong> option. By default, except for the HEADER record, all
147 other unnecessary non ATOM/HETATM records are dropped during the
148 generation of new PDB files. Possible values: <em>yes | no</em>. Default: <em>no</em>.</p>
149 </dd>
150 <dt><strong><strong>-m, --mode </strong> <em>Chains | Sequences | Atoms | CAlphas | AtomNums | AtomsRange | AtomNames | ResidueNums | ResiduesRange | ResidueNames | Distance | NonWater | NonHydrogens</em></strong></dt>
151 <dd>
152 <p>Specify what to extract from <em>PDBFile(s)</em>: <em>Chains</em> - retrieve records for
153 specified chains; <em>Sequences</em> - generate sequence files for specific chains;
154 <em>Atoms</em> - extract atom records; <em>CAlphas</em> - extract atom records for alpha
155 carbon atoms; <em>AtomNums</em> - extract atom records for specified atom numbers;
156 <em>AtomsRange</em> - extract atom records between specified atom number range;
157 <em>AtomNames</em> - extract atom records for specified atom names; <em>ResidueNums</em>
158 - extract records for specified residue numbers; <em>ResiduesRange</em> - extract records
159 for residues between specified residue number range; <em>ResidueNames</em> - extract
160 records for specified residue names; <em>Distance</em> - extract records with in a
161 certain distance from a specific position; <em>NonWater</em> - extract records corresponding
162 to residues other than water; <em>NonHydrogens</em> - extract non-hydrogen records.</p>
163 <p>Possible values: <em>Chains, Sequences Atoms, CAlphas, AtomNums, AtomsRange,
164 AtomNames, ResidueNums, ResiduesRange, ResidueNames, Distance, NonWater,
165 NonHydrogens</em>. Default value: <em>NonWater</em></p>
166 <p>During the generation of new PDB files, unnecessay CONECT records are dropped.</p>
167 <p>For <em>Chains</em> mode, data for appropriate chains specified by <strong>--c --chains</strong> option
168 is extracted from <em>PDBFile(s)</em> and placed into new PDB file(s).</p>
169 <p>For <em>Sequences</em> mode, residues names using various sequence related options are
170 extracted for chains specified by <strong>--c --chains</strong> option from <em>PDBFile(s)</em> and
171 FASTA sequence file(s) are generated.</p>
172 <p>For <em>Distance</em> mode, all ATOM/HETATM records with in a distance specified
173 by <strong>-d --distance</strong> option from a specific atom, residue or a point indicated by
174 <strong>--distancemode</strong> are extracted and placed into new PDB file(s).</p>
175 <p>For <em>NonWater</em> mode, non water ATOM/HETATM record lines, identified using value of
176 <strong>--WaterResidueNames</strong>, are extracted and written to new PDB file(s).</p>
177 <p>For <em>NonHydrogens</em> mode, ATOM/HETATOM record lines containing element symbol
178 other than <em>H</em> are extracted and written to new PDB file(s).</p>
179 <p>For all other options, appropriate ATOM/HETATM records are extracted to generate new
180 PDB file(s).</p>
181 <p><strong>--RecordMode</strong> option controls type of record lines to extract and process from
182 <em>PDBFile(s)</em>: ATOM, HETATM or both.</p>
183 </dd>
184 <dt><strong><strong>--ModifyHeader</strong> <em>yes | no</em></strong></dt>
185 <dd>
186 <p>Specify whether to modify HEADER record during the generation of new PDB files
187 for <strong>-m, --mode</strong> values of <em>Chains | Atoms | CAlphas | Distance</em>. Possible values:
188 <em>yes | no</em>. Default: <em>yes</em>. By default, Classification data is replaced by <em>Data extracted
189 using MayaChemTools</em> before writing out HEADER record.</p>
190 </dd>
191 <dt><strong><strong>--NonStandardKeep</strong> <em>yes | no</em></strong></dt>
192 <dd>
193 <p>Specify whether to include and convert non-standard three letter residue codes into
194 a code specified using <strong>--nonstandardcode</strong> option and include them into sequence file(s)
195 generated during <em>Sequences</em> value of <strong>-m, --mode</strong> option. Possible values: <em>yes | no</em>.
196 Default: <em>yes</em>.</p>
197 <p>A warning is also printed about the presence of non-standard residues. Any residue other
198 than standard 20 amino acids and 5 nucleic acid is considered non-standard; additionally,
199 HETATM residues in chains also tagged as non-standard.</p>
200 </dd>
201 <dt><strong><strong>--NonStandardCode</strong> <em>character</em></strong></dt>
202 <dd>
203 <p>A single character code to use for non-standard residues. Default: <em>X</em>. Possible values:
204 <em>?, -, or X</em>.</p>
205 </dd>
206 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
207 <dd>
208 <p>Overwrite existing files.</p>
209 </dd>
210 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
211 <dd>
212 <p>New PDB and sequence file name is generated using the root: &lt;Root&gt;&lt;Mode&gt;.&lt;Ext&gt;.
213 Default new file name: &lt;PDBFileName&gt;Chain&lt;ChainID&gt;.pdb for <em>Chains</em> <strong>mode</strong>;
214 &lt;PDBFileName&gt;SequenceChain&lt;ChainID&gt;.fasta for <em>Sequences</em> <strong>mode</strong>;
215 &lt;PDBFileName&gt;DistanceBy&lt;DistanceMode&gt;.pdb for <em>Distance</em> <strong>-m, --mode</strong>
216 &lt;PDBFileName&gt;&lt;Mode&gt;.pdb for <em>Atoms | CAlphas | NonWater | NonHydrogens</em> <strong>-m, --mode</strong>
217 values. This option is ignored for multiple input files.</p>
218 </dd>
219 <dt><strong><strong>--RecordMode</strong> <em>Atom | Hetatm | AtomAndHetatm</em></strong></dt>
220 <dd>
221 <p>Specify type of record lines to extract and process from <em>PDBFile(s)</em> during various
222 values of <strong>-m, --mode</strong> option: extract only ATOM record lines; extract only HETATM
223 record lines; extract both ATOM and HETATM lines. Possible values: <em>Atom | Hetatm
224 | AtomAndHetatm | XYZ</em>. Default during <em>Atoms, CAlphas, AtomNums, AtomsRange,
225 AtomNames</em> values of <strong>-m, --mode</strong> option: <em>Atom</em>; otherwise: <em>AtomAndHetatm</em>.</p>
226 <p>This option is ignored during <em>Chains, Sequences</em> values of <strong>-m, --mode</strong> option.</p>
227 </dd>
228 <dt><strong><strong>--Residues</strong> <em>&quot;ResidueNum,[ResidueNum...]&quot; | &quot;StartResidueNum,EndResiduNum&quot; | &quot;ResidueName,[ResidueName...]&quot;</em></strong></dt>
229 <dd>
230 <p>Specify which resiude records to extract from <em>PDBFiles(s)</em> during <em>ResidueNums</em>,
231 <em>ResiduesRange</em>,and <em>ResidueNames</em> value of <strong>-m, --mode</strong> option: extract records
232 corresponding to residue numbers specified in a comma delimited list of residue numbers/names,
233 or with in the range of start and end residue numbers. Possible values: <em>&quot;ResidueNum[,ResidueNum,..]&quot;</em>,
234 <em>StartResidueNum,EndResiduNum</em>, or <em>&lt;&quot;ResidueName[,ResidueName,..]&quot;</em>. Default: <em>None</em>. Examples:</p>
235 <div class="OptionsBox">
236 20
237 <br/> 5,10
238 <br/> TYR,SER,THR</div>
239 <p><strong>--RecordMode</strong> option controls type of record lines to extract from <em>PDBFile(s)</em>:
240 ATOM, HETATM or both.</p>
241 </dd>
242 <dt><strong><strong>--SequenceLength</strong> <em>number</em></strong></dt>
243 <dd>
244 <p>Maximum sequence length per line in sequence file(s). Default: <em>80</em>.</p>
245 </dd>
246 <dt><strong><strong>--SequenceRecords</strong> <em>Atom | SeqRes</em></strong></dt>
247 <dd>
248 <p>Specify which records to use for extracting residue names from <em>PDBFiles(s)</em> during
249 <em>Sequences</em> value of <strong>-m, --mode</strong> option: use ATOM records to compile a list
250 of residues in a chain or parse SEQRES record to get a list of residues. Possible values:
251 <em>Atom | SeqRes</em>. Default: <em>Atom</em>.</p>
252 </dd>
253 <dt><strong><strong>--SequenceIDPrefix</strong> <em>FileName | HeaderRecord | Automatic</em></strong></dt>
254 <dd>
255 <p>Specify how to generate a prefix for sequence IDs during <em>Sequences</em> value
256 of <strong>-m, --mode</strong> option: use input file name prefix; retrieve PDB ID from HEADER record;
257 or automatically decide the method for generating the prefix. The chain IDs are also
258 appended to the prefix. Possible values: <em>FileName | HeaderRecord | Automatic</em>.
259 Default: <em>Automatic</em></p>
260 </dd>
261 <dt><strong><strong>--WaterResidueNames</strong> <em>Automatic | &quot;ResidueName,[ResidueName,...]&quot;</em></strong></dt>
262 <dd>
263 <p>Identification of water residues during <em>NonWater</em> value of <strong>-m, --mode</strong> option. Possible values:
264 <em>Automatic | &quot;ResidueName,[ResidueName,...]&quot;</em>. Default: <em>Automatic</em> - corresponds
265 to &quot;HOH,WAT,H20&quot;. You can also specify a different comma delimited list of residue names
266 to use for water.</p>
267 </dd>
268 <dt><strong><strong>-w, --WorkingDir</strong> <em>dirname</em></strong></dt>
269 <dd>
270 <p>Location of working directory. Default: current directory.</p>
271 </dd>
272 </dl>
273 <p>
274 </p>
275 <h2>EXAMPLES</h2>
276 <p>To extract non-water records from Sample2.pdb file and generate Sample2NonWater.pdb
277 file, type:</p>
278 <div class="ExampleBox">
279 % ExtractFromPDBFiles.pl Sample2.pdb</div>
280 <p>To extract non-water records corresponding to only ATOM records from Sample2.pdb file
281 and generate Sample2NonWater.pdb file, type:</p>
282 <div class="ExampleBox">
283 % ExtractFromPDBFiles.pl --RecordMode Atom Sample2.pdb</div>
284 <p>To extract non-water records from Sample2.pdb file using HOH or WAT residue name for water along
285 with all old non-coordinate records and generate Sample2NewNonWater.pdb file, type:</p>
286 <div class="ExampleBox">
287 % ExtractFromPDBFiles.pl -m NonWater --WaterResidueNames &quot;HOH,WAT&quot;
288 -KeepOldRecords Yes -r Sample2New -o Sample2.pdb</div>
289 <p>To extract non-hydrogens records from Sample2.pdb file and generate Sample2NonHydrogen.pdb
290 file, type:</p>
291 <div class="ExampleBox">
292 % ExtractFromPDBFiles.pl -m NonHydrogens Sample2.pdb</div>
293 <p>To extract data for first chain in Sample2.pdb and generate Sample2ChainA.pdb, type
294 file, type:</p>
295 <div class="ExampleBox">
296 % ExtractFromPDBFiles.pl -m chains -o Sample2.pdb</div>
297 <p>To extract data for both chains in Sample2.pdb and generate Sample2ChainA.pdb and
298 Sample2ChainB.pdb, type:</p>
299 <div class="ExampleBox">
300 % ExtractFromPDBFiles.pl -m chains -c All -o Sample2.pdb</div>
301 <p>To extract data for alpha carbons in Sample2.pdb and generate Sample2CAlphas.pdb, type:</p>
302 <div class="ExampleBox">
303 % ExtractFromPDBFiles.pl -m CAlphas -o Sample2.pdb</div>
304 <p>To extract records for specific residue numbers in all chains from Sample2.pdb file and generate
305 Sample2ResidueNums.pdb file, type:</p>
306 <div class="ExampleBox">
307 % ExtractFromPDBFiles.pl -m ResidueNums --Residues &quot;3,6&quot;
308 Sample2.pdb</div>
309 <p>To extract records for a specific range of residue number in all chains from Sample2.pdb
310 file and generate Sample2ResiduesRange.pdb file, type:</p>
311 <div class="ExampleBox">
312 % ExtractFromPDBFiles.pl -m ResiduesRange --Residues &quot;10,30&quot;
313 Sample2.pdb</div>
314 <p>To extract data for all ATOM and HETATM records with in 10 angstrom of an atom specifed by
315 atom serial number and name &quot;1,N&quot; in Sample2.pdb file and generate Sample2DistanceByAtom.pdb,
316 type:</p>
317 <div class="ExampleBox">
318 % ExtractFromPDBFiles.pl -m Distance --DistanceMode Atom
319 --DistanceOrigin &quot;1,N&quot; -k No --distance 10 -o Sample2.pdb</div>
320 <p>To extract data for all ATOM and HETATM records for complete residues with any atom or hetatm
321 less than 10 angstrom of an atom specifed by atom serial number and name &quot;1,N&quot; in Sample2.pdb
322 file and generate Sample2DistanceByAtom.pdb, type:</p>
323 <div class="ExampleBox">
324 % ExtractFromPDBFiles.pl -m Distance --DistanceMode Atom
325 --DistanceOrigin &quot;1,N&quot; --DistanceSelectionMode ByResidue
326 -k No --distance 10 -o Sample2.pdb</div>
327 <p>To extract data for all ATOM and HETATM records with in 25 angstrom of an arbitrary point &quot;0,0,0&quot;
328 in Sample2.pdb file and generate Sample2DistanceByXYZ.pdb, type:</p>
329 <div class="ExampleBox">
330 % ExtractFromPDBFiles.pl -m Distance --DistanceMode XYZ
331 --DistanceOrigin &quot;0,0,0&quot; -k No --distance 25 -o Sample2.pdb</div>
332 <p>
333 </p>
334 <h2>AUTHOR</h2>
335 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
336 <p>
337 </p>
338 <h2>SEE ALSO</h2>
339 <p><a href="./InfoPDBFiles.html">InfoPDBFiles.pl</a>,&nbsp<a href="./ModifyPDBFiles.html">ModifyPDBFiles.pl</a>
340 </p>
341 <p>
342 </p>
343 <h2>COPYRIGHT</h2>
344 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
345 <p>This file is part of MayaChemTools.</p>
346 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
347 the terms of the GNU Lesser General Public License as published by the Free
348 Software Foundation; either version 3 of the License, or (at your option)
349 any later version.</p>
350 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
351 <table width="100%" border=0 cellpadding=0 cellspacing=2>
352 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./ExtractFromSDFiles.html" title="ExtractFromSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ExtractFromPDBFiles.pl</strong></td></tr>
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