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1 NAME
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2 ModifyPDBFiles.pl - Modify data in PDBFile(s)
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3
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4 SYNOPSIS
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5 ModifyPDBFiles.pl PDBFile(s)...
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6
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7 ModifyPDBFiles.pl [-a, --AtomNumberStart number] [-c, --ChainIDStart
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8 character] [--ChainIDRenameEmpty yes | no] [-h, --help] [-k,
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9 --KeepOldRecords yes | no] [-m, --mode RenumberAtoms | RenumberResidues
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10 | RenumberWaters | RenameChainIDs] [--ModifyHeader yes | no] [-o,
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11 --overwrite] [--ResidueNumberMode Sequential | PerChain]
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12 [--ResidueNumberStart number] [--ResidueNumberHetatmMode automatic |
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13 specify] [--ResidueNumberStarHetatm number] [-r, --root rootname]
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14 [--WaterResidueNames Automatic | "ResidueName, [ResidueName,...]"]
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15 [--WaterResidueStart number] [-w, --WorkingDir dirname] PDBFile(s)...
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16
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17 DESCRIPTION
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18 Modify data in *PDBFile(s)*: renumber atoms, residues, and water
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19 residues or assign new chain IDs. Multiple PDBFile names are separated
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20 by spaces. The valid file extension is *.pdb*. All other file name
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21 extensions are ignored during the wild card expansion. All the PDB files
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22 in a current directory can be specified either by **.pdb* or the current
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23 directory name.
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24
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25 OPTIONS
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26 -a, --AtomNumberStart *number*
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27 Starting atom number to use during *RenumberAtoms* value of -m,
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28 --mode option. Default: *1*. Valid values: positive integers.
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29
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30 -c, --ChainIDStart *character*
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31 A single character to use for starting IDs for chains during
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32 *RenameChainIDs* value of -m, --mode option. Default: *A*. Valid
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33 values: *A to Z*.
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34
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35 --ChainIDRenameEmpty *Yes | No*
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36 Specify whether to rename empty chain IDs during *RenameChainIDs*
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37 -m, --mode value. By default, ATOM and HETATM records with no chain
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38 IDs are left unchanged. Possible values: *yes | no*. Default: *No*.
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39
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40 -h, --help
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41 Print this help message.
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42
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43 -k, --KeepOldRecords *yes | no*
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44 Specify whether to transfer old non ATOM and HETATM records from
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45 input PDBFile(s) to new PDBFile(s). By default, except for the
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46 HEADER record, all records other than ATOM/HETATM are dropped during
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47 the generation of new PDB files. Possible values: *yes | no*.
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48 Default: *no*.
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49
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50 -m, --mode *RenumberAtoms | RenumberResidues | RenumberWaters |
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51 RenameChainIDs*
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52 Specify how to modify *PDBFile(s)*. Possible values: *RenumberAtoms
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53 | RenumberResidues | RenumberWaters | RenameChainIDs*. Default:
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54 *RenumberResidues*.
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55
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56 For *RenumberAtoms* mode, residue number in ATOM and HETATM records
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57 are reassigned sequentially starting using value of -a,
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58 --AtomNumberStart option.
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59
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60 For *RenumberResidues* mode, serial number in ATOM and HETATM
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61 records are reassigned either sequentially or statring from
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62 specified values for ATOM and HETATM records in each chain.
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63
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64 For *RenumberWaters* mode, residue number for waters are reassigned
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65 starting from a specific value.
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66
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67 For *RenameChainIDs* mode, all the chain IDs are reassigned starting
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68 from a specific chain ID.
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69
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70 During the generation of new PDB files, unnecessary CONECT records
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71 are dropped.
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72
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73 --ModifyHeader *yes | no*
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74 Specify whether to modify HEADER record during the generation of new
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75 PDB files Possible values: *yes | no*. Default: *yes*. By defailt,
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76 Classification data is replaced by *Data modified using
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77 MayaChemTools* before writing out HEADER record.
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78
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79 -o, --overwrite
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80 Overwrite existing files
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81
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82 --ResidueNumberMode *Sequential | PerChain*
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83 Specify how to renumber residues: renumber residues sequentially
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84 across all the chains or start from the begining for each chain.
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85 Possible values: *Sequential | PerChain*. Default: *PerChain*.
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86
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87 --ResidueNumberStart *number*
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88 Starting residue number to use for ATOM records in chains. Default:
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89 *1*. Valid values positive integers.
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90
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91 For *Sequential* value of --ResidueNumberMode option, residue
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92 numbers are assigned sequentially across all the chains starting
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93 from the specified value.
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94
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95 For *PerChain* value of --ResidueNumberMode option, residue numbers
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96 are starting again from the specified value for each chain.
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97
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98 HETATM residues with in the chains are numbered using this value as
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99 well
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100
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101 --ResidueNumberHetatmMode *automatic | specify*
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102 Specify how to start residue number for HETATM records: use the next
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103 sequential residue number after the last residue number from ATOM
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104 records or start from a specific residue number. Possible values:
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105 *automatic | specify*. Default: *automatic*
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106
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107 For *automatic* , residue number after highest residue number of
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108 ATOM records is used as the starting residue number for HETATM
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109 records.
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110
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111 For *specify*, value of option --ResidueNumberStarHetatm is used as
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112 the starting residue number for HETATM records.
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113
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114 This option along with --ResidueNumberStartHetatm only applies to
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115 HETATM records outside the chains.
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116
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117 --ResidueNumberStartHetatm *number*
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118 Starting residue number to use for HETATM records. Default: *6000*.
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119 Valid values positive integers.
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120
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121 -r, --root *rootname*
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122 New PDB and sequence file name is generated using the root:
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123 <Root><Mode>.<Ext>. Default new file name: <PDBFileName><Mode>.pdb.
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124 This option is ignored for multiple input files.
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125
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126 --WaterResidueNames *Automatic | "ResidueName,[ResidueName,...]"*
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127 Identification of water residues during *RenumberWaters* value of
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128 -m, --mode option. Possible values: *Automatic |
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129 "ResidueName,[ResidueName,...]"*. Default: *Automatic* which
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130 corresponds to "HOH,WAT,H20". You can also specify a different comma
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131 delimited list of residue names to use for water.
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132
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133 --WaterResidueStart *number*
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134 Starting water residue number to use during *RenumberWaters* -m,
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135 --mode value. Default: *8000*. Valid values: positive integers.
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136
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137 -w, --WorkingDir *dirname*
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138 Location of working directory. Default: current directory.
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139
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140 EXAMPLES
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141 To renumber ATOM and HETATM residues starting from 1 for each chain with
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142 continuation to HETATM residues outside TER records in Sample2.pdb and
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143 generate Sample2RenumberResidues.pdb file, type:
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144
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145 % ModifyPDBFiles.pl Sample1.pdb
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146
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147 To renumber ATOM and HETATM residues sequentially across all chains
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148 starting from 1 with continuation to HETATM residues outside TER records
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149 in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type:
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150
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151 % ModifyPDBFiles.pl --ResidueNumberMode Sequential -o Sample1.pdb
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152
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153 To renumber ATOM and HETATM residues sequentially across all chains
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154 starting from 1 and HETATM residues outside TER records starting from
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155 6000 in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type:
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156
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157 % ModifyPDBFiles.pl --ResidueNumberMode Sequential
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158 --ResidueNumberHetatmMode Specify -o Sample1.pdb
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159
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160 To renumber ATOM and HETATM residues sequentially across all chains
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161 starting from 100 for ATOM/HETATM residues with in TER records and
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162 starting from 999 for HETATM residues outside TER records in Sample2.pdb
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163 and generate Sample2RenumberResidues.pdb file, type:
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164
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165 % ModifyPDBFiles.pl --ResidueNumberMode Sequential
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166 --ResidueNumberHetatmMode Specify --ResidueNumberStart 100
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167 --ResidueNumberStartHetatm 999 -o Sample2.pdb
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168
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169 To renumber ATOM and HETATM residues from 100 for each chain and
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170 starting from 999 for HETATM residues outside TER records in Sample2.pdb
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171 and generate Sample2RenumberResidues.pdb file, type:
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172
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173 % ModifyPDBFiles.pl --ResidueNumberMode PerChain
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174 --ResidueNumberHetatmMode Specify --ResidueNumberStart 100
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175 --ResidueNumberStartHetatm 999 -o Sample2.pdb
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176
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177 To renumber ATOM serial numbers sequentially starting from 100 in
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178 Sample1.pdb file and generate Sample1RenumberAtoms.pdb file, type:
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179
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180 % ModifyPDBFiles.pl -m RenumberAtoms --AtomNumberStart 100
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181 -o Sample1.pdb
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182
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183 To renumber water residues identified by "HOH,WAT" starting from residue
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184 number 1000 in Sample2.pdb file and generate Sample2RenumberWaters.pdb
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185 file, type:
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186
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187 % ModifyPDBFiles.pl -m RenumberWaters --WaterResidueNames "HOH,WAT"
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188 -o --WaterResidueStart 950 Sample2.pdb
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189
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190 To rename all chain IDs starting from A in Sample1.pdb file and generate
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191 Sample1RenameChainIDs.pdb file, type:
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192
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193 % ModifyPDBFiles.pl -m RenameChainIDs -o Sample1.pdb
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194
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195 To rename all chain IDs starting from B without assigning any chain IDs
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196 to ATOM/HETATOM with no chain IDs in Sample2.pdb file and generate
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197 Sample2RenameChainIDs.pdb file, type:
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198
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199 % ModifyPDBFiles.pl l -m RenameChainIDs -c B --ChainIDRenameEmpty No
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200 -o Sample2.pdb
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201
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202 AUTHOR
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203 Manish Sud <msud@san.rr.com>
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204
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205 SEE ALSO
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206 ExtractFromPDBFiles.pl, InfoPDBFiles.pl
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207
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208 COPYRIGHT
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209 Copyright (C) 2015 Manish Sud. All rights reserved.
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210
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211 This file is part of MayaChemTools.
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212
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213 MayaChemTools is free software; you can redistribute it and/or modify it
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214 under the terms of the GNU Lesser General Public License as published by
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215 the Free Software Foundation; either version 3 of the License, or (at
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216 your option) any later version.
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217
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