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3 <title>MayaChemTools:Documentation:ExtractFromPDBFiles.pl</title>
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/ExtractFromPDBFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ExtractFromPDBFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ExtractFromPDBFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ExtractFromPDBFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>ExtractFromPDBFiles.pl - Extract specific data from PDBFile(s)</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>ExtractFromPDBFiles.pl PDBFile(s)...</p>
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26 <p>ExtractFromPDBFiles.pl [<strong>-a, --Atoms</strong> "AtomNum, [AtomNum...]" | "StartAtomNum, EndAtomNum" |
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27 "AtomName, [AtomName...]"] [<strong>-c, --chains</strong> First | All | "ChainID, [ChainID,...]"]
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28 [<--CombineChains> yes | no] [<strong>-d, --distance</strong> number] [<strong>--DistanceMode</strong> Atom | Hetatm | Residue | XYZ]
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29 [<strong>--DistanceOrigin</strong> "AtomNumber, AtomName" | "HetatmNumber, HetAtmName" | "ResidueNumber, ResidueName, [ChainID]" | "X,Y,Z">]
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30 [<--DistanceSelectionMode> ByAtom | ByResidue] [<strong>-h, --help</strong>] [<strong>-k, --KeepOldRecords</strong> yes | no]
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31 [<strong>-m, --mode </strong> Chains | Sequences | Atoms | CAlphas | AtomNums | AtomsRange | AtomNames |
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32 ResidueNums | ResiduesRange | ResidueNames | Distance | NonWater | NonHydrogens]
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33 [<strong>--ModifyHeader</strong> yes | no] [<strong>--NonStandardKeep</strong> yes | no] [<strong>--NonStandardCode</strong> character]
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34 [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname] <strong>--RecordMode</strong> <em>Atom | Hetatm | AtomAndHetatm</em>]
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35 [<strong>--Residues</strong> "ResidueNum,[ResidueNum...]" | StartResidueNum,EndResiduNum ]
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36 [<strong>--SequenceLength</strong> number] [<strong>--SequenceRecords</strong> Atom | SeqRes]
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37 [<strong>--SequenceIDPrefix</strong> FileName | HeaderRecord | Automatic]
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38 [<strong>--WaterResidueNames</strong> Automatic | "ResidueName, [ResidueName,...]"]
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39 [<strong>-w, --WorkingDir</strong> dirname] PDBFile(s)...</p>
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40 <p>
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41 </p>
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42 <h2>DESCRIPTION</h2>
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43 <p>Extract specific data from <em>PDBFile(s)</em> and generate appropriate PDB or sequence file(s).
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44 Multiple PDBFile names are separated by spaces. The valid file extension is <em>.pdb</em>.
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45 All other file name extensions are ignored during the wild card expansion. All the PDB files
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46 in a current directory can be specified either by <em>*.pdb</em> or the current directory name.</p>
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47 <p>During <em>Chains</em> and <em>Sequences</em> values of <strong>-m, --mode</strong> option, all ATOM/HETAM records
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48 for chains after the first model in PDB fils containing data for multiple models are ignored.</p>
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49 <p>
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50 </p>
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51 <h2>OPTIONS</h2>
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52 <dl>
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53 <dt><strong><strong>-a, --Atoms</strong> <em>"AtomNum,[AtomNum...]" | "StartAtomNum,EndAtomNum" | "AtomName,[AtomName...]"</em></strong></dt>
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54 <dd>
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55 <p>Specify which atom records to extract from <em>PDBFiles(s)</em> during <em>AtomNums</em>,
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56 <em>AtomsRange</em>, and <em>AtomNames</em> value of <strong>-m, --mode</strong> option: extract records
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57 corresponding to atom numbers specified in a comma delimited list of atom numbers/names,
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58 or with in the range of start and end atom numbers. Possible values: <em>"AtomNum[,AtomNum,..]"</em>,
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59 <em>StartAtomNum,EndAtomNum</em>, or <em>"AtomName[,AtomName,..]"</em>. Default: <em>None</em>. Examples:</p>
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60 <div class="OptionsBox">
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61 10
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62 <br/> 15,20
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63 <br/> N,CA,C,O</div>
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64 </dd>
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65 <dt><strong><strong>-c, --chains</strong> <em>First | All | ChainID,[ChainID,...]</em></strong></dt>
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66 <dd>
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67 <p>Specify which chains to extract from <em>PDBFile(s)</em> during <em>Chains | Sequences</em> value of
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68 <strong>-m, --mode</strong> option: first chain, all chains, or a specific list of comma delimited chain IDs.
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69 Possible values: <em>First | All | ChainID,[ChainID,...]</em>. Default: <em>First</em>. Examples:</p>
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70 <div class="OptionsBox">
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71 A
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72 <br/> A,B
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73 <br/> All</div>
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74 </dd>
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75 <dt><strong><strong>--CombineChains</strong> <em>yes | no</em></strong></dt>
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76 <dd>
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77 <p>Specify whether to combine extracted chains data into a single file during <em>Chains</em> or
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78 <em>Sequences</em> value of <strong>-m, --mode</strong> option. Possible values: <em>yes | no</em>. Default: <em>no</em>.</p>
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79 <p>During <em>Chains</em> value of <-m, --mode> option with <em>Yes</em> value of <--CombineChains>,
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80 extracted data for specified chains is written into a single file instead of individual file for each
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81 chain.</p>
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82 <p>During <em>Sequences</em> value of <-m, --mode> option with <em>Yes</em> value of <--CombineChains>,
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83 residues sequences for specified chains are extracted and concatenated into a single sequence
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84 file instead of individual file for each chain.</p>
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85 </dd>
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86 <dt><strong><strong>-d, --distance</strong> <em>number</em></strong></dt>
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87 <dd>
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88 <p>Specify distance used to extract ATOM/HETATM recods during <em>Distance</em> value of
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89 <strong>-m, --mode</strong> option. Default: <em>10.0</em> angstroms.</p>
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90 <p><strong>--RecordMode</strong> option controls type of record lines to extract from <em>PDBFile(s)</em>:
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91 ATOM, HETATM or both.</p>
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92 </dd>
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93 <dt><strong><strong>--DistanceMode</strong> <em>Atom | Hetatm | Residue | XYZ</em></strong></dt>
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94 <dd>
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95 <p>Specify how to extract ATOM/HETATM records from <em>PDBFile(s)</em> during <em>Distance</em> value of
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96 <strong>-m, --mode</strong> option: extract all the records within a certain distance specifed by <strong>-d, --distance</strong>
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97 from an atom or hetro atom record, a residue, or any artbitrary point. Possible values: <em>Atom |
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98 Hetatm | Residue | XYZ</em>. Default: <em>XYZ</em>.</p>
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99 <p>During <em>Residue</em> value of <strong>--distancemode</strong>, distance of ATOM/HETATM records is calculated from
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100 all the atoms in the residue and the records are selected as long as any atom of the residue lies with
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101 in the distace specified using <strong>-d, --distance</strong> option.</p>
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102 <p><strong>--RecordMode</strong> option controls type of record lines to extract from <em>PDBFile(s)</em>:
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103 ATOM, HETATM or both.</p>
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104 </dd>
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105 <dt><strong><strong>--DistanceSelectionMode</strong> <em>ByAtom | ByResidue</em></strong></dt>
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106 <dd>
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107 <p>Specify how how to extract ATOM/HETATM records from <em>PDBFile(s)</em> during <em>Distance</em> value of
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108 <strong>-m, --mode</strong> option for all values of <strong>--DistanceMode</strong> option: extract only those ATOM/HETATM
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109 records that meet specified distance criterion; extract all records corresponding to a residue as
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110 long as one of the ATOM/HETATM record in the residue satisfies specified distance criterion. Possible
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111 values: <em>ByAtom, ByResidue</em>. Default value: <em>ByAtom</em>.</p>
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112 </dd>
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113 <dt><strong><strong>--DistanceOrigin</strong> <em>"AtomNumber,AtomName" | "HetatmNumber,HetAtmName" | "ResidueNumber,ResidueName[,ChainID]" | "X,Y,Z"</em></strong></dt>
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114 <dd>
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115 <p>This value is <strong>--distancemode</strong> specific. In general, it identifies a point used to select
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116 other ATOM/HETATMS with in a specific distance from this point.</p>
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117 <p>For <em>Atom</em> value of <strong>--distancemode</strong>, this option corresponds to an atom specification.
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118 Format: <em>AtomNumber,AtomName</em>. Example:</p>
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119 <div class="OptionsBox">
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120 455,CA</div>
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121 <p>For <em>Hetatm</em> value of <strong>--distancemode</strong>, this option corresponds to a hetatm specification.
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122 Format: <em>HetatmNumber,HetAtmName</em>. Example:</p>
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123 <div class="OptionsBox">
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124 5295,C1</div>
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125 <p>For <em>Residue</em> value of <strong>--distancemode</strong>, this option corresponds to a residue specification.
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126 Format: <em>ResidueNumber, ResidueName[,ChainID]</em>. Example:</p>
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127 <div class="OptionsBox">
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128 78,MSE
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129 <br/> 977,RET,A
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130 <br/> 978,RET,B</div>
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131 <p>For <em>XYZ</em> value of <strong>--distancemode</strong>, this option corresponds to a coordinate of an
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132 arbitrary point. Format: <em>X,Y,X</em>. Example:</p>
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133 <div class="OptionsBox">
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134 10.044,19.261,-4.292</div>
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135 <p><strong>--RecordMode</strong> option controls type of record lines to extract from <em>PDBFile(s)</em>:
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136 ATOM, HETATM or both.</p>
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137 </dd>
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138 <dt><strong><strong>-h, --help</strong></strong></dt>
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139 <dd>
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140 <p>Print this help message.</p>
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141 </dd>
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142 <dt><strong><strong>-k, --KeepOldRecords</strong> <em>yes | no</em></strong></dt>
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143 <dd>
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144 <p>Specify whether to transfer old non ATOM and HETATM records from input PDBFile(s) to new
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145 PDBFile(s) during <em>Chains | Atoms | HetAtms | CAlphas | Distance| NonWater | NonHydrogens</em>
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146 value of <strong>-m --mode</strong> option. By default, except for the HEADER record, all
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147 other unnecessary non ATOM/HETATM records are dropped during the
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148 generation of new PDB files. Possible values: <em>yes | no</em>. Default: <em>no</em>.</p>
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149 </dd>
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150 <dt><strong><strong>-m, --mode </strong> <em>Chains | Sequences | Atoms | CAlphas | AtomNums | AtomsRange | AtomNames | ResidueNums | ResiduesRange | ResidueNames | Distance | NonWater | NonHydrogens</em></strong></dt>
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151 <dd>
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152 <p>Specify what to extract from <em>PDBFile(s)</em>: <em>Chains</em> - retrieve records for
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153 specified chains; <em>Sequences</em> - generate sequence files for specific chains;
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154 <em>Atoms</em> - extract atom records; <em>CAlphas</em> - extract atom records for alpha
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155 carbon atoms; <em>AtomNums</em> - extract atom records for specified atom numbers;
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156 <em>AtomsRange</em> - extract atom records between specified atom number range;
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157 <em>AtomNames</em> - extract atom records for specified atom names; <em>ResidueNums</em>
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158 - extract records for specified residue numbers; <em>ResiduesRange</em> - extract records
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159 for residues between specified residue number range; <em>ResidueNames</em> - extract
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160 records for specified residue names; <em>Distance</em> - extract records with in a
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161 certain distance from a specific position; <em>NonWater</em> - extract records corresponding
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162 to residues other than water; <em>NonHydrogens</em> - extract non-hydrogen records.</p>
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163 <p>Possible values: <em>Chains, Sequences Atoms, CAlphas, AtomNums, AtomsRange,
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164 AtomNames, ResidueNums, ResiduesRange, ResidueNames, Distance, NonWater,
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165 NonHydrogens</em>. Default value: <em>NonWater</em></p>
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166 <p>During the generation of new PDB files, unnecessay CONECT records are dropped.</p>
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167 <p>For <em>Chains</em> mode, data for appropriate chains specified by <strong>--c --chains</strong> option
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168 is extracted from <em>PDBFile(s)</em> and placed into new PDB file(s).</p>
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169 <p>For <em>Sequences</em> mode, residues names using various sequence related options are
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170 extracted for chains specified by <strong>--c --chains</strong> option from <em>PDBFile(s)</em> and
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171 FASTA sequence file(s) are generated.</p>
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172 <p>For <em>Distance</em> mode, all ATOM/HETATM records with in a distance specified
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173 by <strong>-d --distance</strong> option from a specific atom, residue or a point indicated by
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174 <strong>--distancemode</strong> are extracted and placed into new PDB file(s).</p>
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175 <p>For <em>NonWater</em> mode, non water ATOM/HETATM record lines, identified using value of
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176 <strong>--WaterResidueNames</strong>, are extracted and written to new PDB file(s).</p>
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177 <p>For <em>NonHydrogens</em> mode, ATOM/HETATOM record lines containing element symbol
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178 other than <em>H</em> are extracted and written to new PDB file(s).</p>
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179 <p>For all other options, appropriate ATOM/HETATM records are extracted to generate new
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180 PDB file(s).</p>
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181 <p><strong>--RecordMode</strong> option controls type of record lines to extract and process from
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182 <em>PDBFile(s)</em>: ATOM, HETATM or both.</p>
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183 </dd>
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184 <dt><strong><strong>--ModifyHeader</strong> <em>yes | no</em></strong></dt>
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185 <dd>
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186 <p>Specify whether to modify HEADER record during the generation of new PDB files
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187 for <strong>-m, --mode</strong> values of <em>Chains | Atoms | CAlphas | Distance</em>. Possible values:
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188 <em>yes | no</em>. Default: <em>yes</em>. By default, Classification data is replaced by <em>Data extracted
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189 using MayaChemTools</em> before writing out HEADER record.</p>
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190 </dd>
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191 <dt><strong><strong>--NonStandardKeep</strong> <em>yes | no</em></strong></dt>
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192 <dd>
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193 <p>Specify whether to include and convert non-standard three letter residue codes into
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194 a code specified using <strong>--nonstandardcode</strong> option and include them into sequence file(s)
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195 generated during <em>Sequences</em> value of <strong>-m, --mode</strong> option. Possible values: <em>yes | no</em>.
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196 Default: <em>yes</em>.</p>
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197 <p>A warning is also printed about the presence of non-standard residues. Any residue other
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198 than standard 20 amino acids and 5 nucleic acid is considered non-standard; additionally,
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199 HETATM residues in chains also tagged as non-standard.</p>
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200 </dd>
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201 <dt><strong><strong>--NonStandardCode</strong> <em>character</em></strong></dt>
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202 <dd>
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203 <p>A single character code to use for non-standard residues. Default: <em>X</em>. Possible values:
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204 <em>?, -, or X</em>.</p>
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205 </dd>
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206 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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207 <dd>
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208 <p>Overwrite existing files.</p>
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209 </dd>
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210 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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211 <dd>
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212 <p>New PDB and sequence file name is generated using the root: <Root><Mode>.<Ext>.
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213 Default new file name: <PDBFileName>Chain<ChainID>.pdb for <em>Chains</em> <strong>mode</strong>;
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214 <PDBFileName>SequenceChain<ChainID>.fasta for <em>Sequences</em> <strong>mode</strong>;
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215 <PDBFileName>DistanceBy<DistanceMode>.pdb for <em>Distance</em> <strong>-m, --mode</strong>
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216 <PDBFileName><Mode>.pdb for <em>Atoms | CAlphas | NonWater | NonHydrogens</em> <strong>-m, --mode</strong>
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217 values. This option is ignored for multiple input files.</p>
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218 </dd>
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219 <dt><strong><strong>--RecordMode</strong> <em>Atom | Hetatm | AtomAndHetatm</em></strong></dt>
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220 <dd>
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221 <p>Specify type of record lines to extract and process from <em>PDBFile(s)</em> during various
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222 values of <strong>-m, --mode</strong> option: extract only ATOM record lines; extract only HETATM
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223 record lines; extract both ATOM and HETATM lines. Possible values: <em>Atom | Hetatm
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224 | AtomAndHetatm | XYZ</em>. Default during <em>Atoms, CAlphas, AtomNums, AtomsRange,
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225 AtomNames</em> values of <strong>-m, --mode</strong> option: <em>Atom</em>; otherwise: <em>AtomAndHetatm</em>.</p>
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226 <p>This option is ignored during <em>Chains, Sequences</em> values of <strong>-m, --mode</strong> option.</p>
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227 </dd>
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228 <dt><strong><strong>--Residues</strong> <em>"ResidueNum,[ResidueNum...]" | "StartResidueNum,EndResiduNum" | "ResidueName,[ResidueName...]"</em></strong></dt>
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229 <dd>
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230 <p>Specify which resiude records to extract from <em>PDBFiles(s)</em> during <em>ResidueNums</em>,
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231 <em>ResiduesRange</em>,and <em>ResidueNames</em> value of <strong>-m, --mode</strong> option: extract records
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232 corresponding to residue numbers specified in a comma delimited list of residue numbers/names,
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233 or with in the range of start and end residue numbers. Possible values: <em>"ResidueNum[,ResidueNum,..]"</em>,
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234 <em>StartResidueNum,EndResiduNum</em>, or <em><"ResidueName[,ResidueName,..]"</em>. Default: <em>None</em>. Examples:</p>
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235 <div class="OptionsBox">
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236 20
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237 <br/> 5,10
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238 <br/> TYR,SER,THR</div>
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239 <p><strong>--RecordMode</strong> option controls type of record lines to extract from <em>PDBFile(s)</em>:
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240 ATOM, HETATM or both.</p>
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241 </dd>
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242 <dt><strong><strong>--SequenceLength</strong> <em>number</em></strong></dt>
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243 <dd>
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244 <p>Maximum sequence length per line in sequence file(s). Default: <em>80</em>.</p>
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245 </dd>
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246 <dt><strong><strong>--SequenceRecords</strong> <em>Atom | SeqRes</em></strong></dt>
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247 <dd>
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248 <p>Specify which records to use for extracting residue names from <em>PDBFiles(s)</em> during
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249 <em>Sequences</em> value of <strong>-m, --mode</strong> option: use ATOM records to compile a list
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250 of residues in a chain or parse SEQRES record to get a list of residues. Possible values:
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251 <em>Atom | SeqRes</em>. Default: <em>Atom</em>.</p>
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252 </dd>
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253 <dt><strong><strong>--SequenceIDPrefix</strong> <em>FileName | HeaderRecord | Automatic</em></strong></dt>
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254 <dd>
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255 <p>Specify how to generate a prefix for sequence IDs during <em>Sequences</em> value
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256 of <strong>-m, --mode</strong> option: use input file name prefix; retrieve PDB ID from HEADER record;
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257 or automatically decide the method for generating the prefix. The chain IDs are also
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258 appended to the prefix. Possible values: <em>FileName | HeaderRecord | Automatic</em>.
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259 Default: <em>Automatic</em></p>
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260 </dd>
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261 <dt><strong><strong>--WaterResidueNames</strong> <em>Automatic | "ResidueName,[ResidueName,...]"</em></strong></dt>
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262 <dd>
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263 <p>Identification of water residues during <em>NonWater</em> value of <strong>-m, --mode</strong> option. Possible values:
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264 <em>Automatic | "ResidueName,[ResidueName,...]"</em>. Default: <em>Automatic</em> - corresponds
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265 to "HOH,WAT,H20". You can also specify a different comma delimited list of residue names
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266 to use for water.</p>
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267 </dd>
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268 <dt><strong><strong>-w, --WorkingDir</strong> <em>dirname</em></strong></dt>
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269 <dd>
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270 <p>Location of working directory. Default: current directory.</p>
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271 </dd>
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272 </dl>
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273 <p>
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274 </p>
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275 <h2>EXAMPLES</h2>
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276 <p>To extract non-water records from Sample2.pdb file and generate Sample2NonWater.pdb
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277 file, type:</p>
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278 <div class="ExampleBox">
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279 % ExtractFromPDBFiles.pl Sample2.pdb</div>
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280 <p>To extract non-water records corresponding to only ATOM records from Sample2.pdb file
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281 and generate Sample2NonWater.pdb file, type:</p>
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282 <div class="ExampleBox">
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283 % ExtractFromPDBFiles.pl --RecordMode Atom Sample2.pdb</div>
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284 <p>To extract non-water records from Sample2.pdb file using HOH or WAT residue name for water along
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285 with all old non-coordinate records and generate Sample2NewNonWater.pdb file, type:</p>
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286 <div class="ExampleBox">
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287 % ExtractFromPDBFiles.pl -m NonWater --WaterResidueNames "HOH,WAT"
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288 -KeepOldRecords Yes -r Sample2New -o Sample2.pdb</div>
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289 <p>To extract non-hydrogens records from Sample2.pdb file and generate Sample2NonHydrogen.pdb
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290 file, type:</p>
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291 <div class="ExampleBox">
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292 % ExtractFromPDBFiles.pl -m NonHydrogens Sample2.pdb</div>
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293 <p>To extract data for first chain in Sample2.pdb and generate Sample2ChainA.pdb, type
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294 file, type:</p>
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295 <div class="ExampleBox">
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296 % ExtractFromPDBFiles.pl -m chains -o Sample2.pdb</div>
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297 <p>To extract data for both chains in Sample2.pdb and generate Sample2ChainA.pdb and
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298 Sample2ChainB.pdb, type:</p>
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299 <div class="ExampleBox">
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300 % ExtractFromPDBFiles.pl -m chains -c All -o Sample2.pdb</div>
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301 <p>To extract data for alpha carbons in Sample2.pdb and generate Sample2CAlphas.pdb, type:</p>
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302 <div class="ExampleBox">
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303 % ExtractFromPDBFiles.pl -m CAlphas -o Sample2.pdb</div>
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304 <p>To extract records for specific residue numbers in all chains from Sample2.pdb file and generate
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305 Sample2ResidueNums.pdb file, type:</p>
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306 <div class="ExampleBox">
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307 % ExtractFromPDBFiles.pl -m ResidueNums --Residues "3,6"
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308 Sample2.pdb</div>
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309 <p>To extract records for a specific range of residue number in all chains from Sample2.pdb
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310 file and generate Sample2ResiduesRange.pdb file, type:</p>
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311 <div class="ExampleBox">
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312 % ExtractFromPDBFiles.pl -m ResiduesRange --Residues "10,30"
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313 Sample2.pdb</div>
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314 <p>To extract data for all ATOM and HETATM records with in 10 angstrom of an atom specifed by
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315 atom serial number and name "1,N" in Sample2.pdb file and generate Sample2DistanceByAtom.pdb,
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316 type:</p>
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317 <div class="ExampleBox">
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318 % ExtractFromPDBFiles.pl -m Distance --DistanceMode Atom
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319 --DistanceOrigin "1,N" -k No --distance 10 -o Sample2.pdb</div>
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320 <p>To extract data for all ATOM and HETATM records for complete residues with any atom or hetatm
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321 less than 10 angstrom of an atom specifed by atom serial number and name "1,N" in Sample2.pdb
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322 file and generate Sample2DistanceByAtom.pdb, type:</p>
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323 <div class="ExampleBox">
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324 % ExtractFromPDBFiles.pl -m Distance --DistanceMode Atom
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325 --DistanceOrigin "1,N" --DistanceSelectionMode ByResidue
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326 -k No --distance 10 -o Sample2.pdb</div>
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327 <p>To extract data for all ATOM and HETATM records with in 25 angstrom of an arbitrary point "0,0,0"
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328 in Sample2.pdb file and generate Sample2DistanceByXYZ.pdb, type:</p>
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329 <div class="ExampleBox">
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330 % ExtractFromPDBFiles.pl -m Distance --DistanceMode XYZ
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331 --DistanceOrigin "0,0,0" -k No --distance 25 -o Sample2.pdb</div>
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332 <p>
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333 </p>
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334 <h2>AUTHOR</h2>
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335 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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336 <p>
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337 </p>
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338 <h2>SEE ALSO</h2>
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339 <p><a href="./InfoPDBFiles.html">InfoPDBFiles.pl</a>, <a href="./ModifyPDBFiles.html">ModifyPDBFiles.pl</a>
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340 </p>
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341 <p>
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342 </p>
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343 <h2>COPYRIGHT</h2>
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344 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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345 <p>This file is part of MayaChemTools.</p>
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346 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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347 the terms of the GNU Lesser General Public License as published by the Free
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348 Software Foundation; either version 3 of the License, or (at your option)
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349 any later version.</p>
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350 <p> </p><p> </p><div class="DocNav">
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351 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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352 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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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353 </table>
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354 </div>
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355 <br />
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356 <center>
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357 <img src="../../images/h2o2.png">
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358 </center>
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359 </body>
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360 </html>
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