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