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1 NAME
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2 ExtractFromPDBFiles.pl - Extract specific data from PDBFile(s)
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3
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4 SYNOPSIS
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5 ExtractFromPDBFiles.pl PDBFile(s)...
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6
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7 ExtractFromPDBFiles.pl [-a, --Atoms "AtomNum, [AtomNum...]" |
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8 "StartAtomNum, EndAtomNum" | "AtomName, [AtomName...]"] [-c, --chains
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9 First | All | "ChainID, [ChainID,...]"] [<--CombineChains> yes | no]
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10 [-d, --distance number] [--DistanceMode Atom | Hetatm | Residue | XYZ]
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11 [--DistanceOrigin "AtomNumber, AtomName" | "HetatmNumber, HetAtmName" |
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12 "ResidueNumber, ResidueName, [ChainID]" | "X,Y,Z">]
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13 [<--DistanceSelectionMode> ByAtom | ByResidue] [-h, --help] [-k,
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14 --KeepOldRecords yes | no] [-m, --mode Chains | Sequences | Atoms |
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15 CAlphas | AtomNums | AtomsRange | AtomNames | ResidueNums |
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16 ResiduesRange | ResidueNames | Distance | NonWater | NonHydrogens]
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17 [--ModifyHeader yes | no] [--NonStandardKeep yes | no]
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18 [--NonStandardCode character] [-o, --overwrite] [-r, --root rootname]
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19 --RecordMode *Atom | Hetatm | AtomAndHetatm*] [--Residues
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20 "ResidueNum,[ResidueNum...]" | StartResidueNum,EndResiduNum ]
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21 [--SequenceLength number] [--SequenceRecords Atom | SeqRes]
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22 [--SequenceIDPrefix FileName | HeaderRecord | Automatic]
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23 [--WaterResidueNames Automatic | "ResidueName, [ResidueName,...]"] [-w,
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24 --WorkingDir dirname] PDBFile(s)...
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25
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26 DESCRIPTION
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27 Extract specific data from *PDBFile(s)* and generate appropriate PDB or
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28 sequence file(s). Multiple PDBFile names are separated by spaces. The
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29 valid file extension is *.pdb*. All other file name extensions are
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30 ignored during the wild card expansion. All the PDB files in a current
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31 directory can be specified either by **.pdb* or the current directory
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32 name.
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33
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34 During *Chains* and *Sequences* values of -m, --mode option, all
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35 ATOM/HETAM records for chains after the first model in PDB fils
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36 containing data for multiple models are ignored.
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37
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38 OPTIONS
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39 -a, --Atoms *"AtomNum,[AtomNum...]" | "StartAtomNum,EndAtomNum" |
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40 "AtomName,[AtomName...]"*
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41 Specify which atom records to extract from *PDBFiles(s)* during
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42 *AtomNums*, *AtomsRange*, and *AtomNames* value of -m, --mode
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43 option: extract records corresponding to atom numbers specified in a
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44 comma delimited list of atom numbers/names, or with in the range of
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45 start and end atom numbers. Possible values:
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46 *"AtomNum[,AtomNum,..]"*, *StartAtomNum,EndAtomNum*, or
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47 *"AtomName[,AtomName,..]"*. Default: *None*. Examples:
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48
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49 10
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50 15,20
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51 N,CA,C,O
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52
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53 -c, --chains *First | All | ChainID,[ChainID,...]*
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54 Specify which chains to extract from *PDBFile(s)* during *Chains |
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55 Sequences* value of -m, --mode option: first chain, all chains, or a
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56 specific list of comma delimited chain IDs. Possible values: *First
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57 | All | ChainID,[ChainID,...]*. Default: *First*. Examples:
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58
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59 A
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60 A,B
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61 All
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62
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63 --CombineChains *yes | no*
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64 Specify whether to combine extracted chains data into a single file
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65 during *Chains* or *Sequences* value of -m, --mode option. Possible
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66 values: *yes | no*. Default: *no*.
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67
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68 During *Chains* value of <-m, --mode> option with *Yes* value of
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69 <--CombineChains>, extracted data for specified chains is written
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70 into a single file instead of individual file for each chain.
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71
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72 During *Sequences* value of <-m, --mode> option with *Yes* value of
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73 <--CombineChains>, residues sequences for specified chains are
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74 extracted and concatenated into a single sequence file instead of
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75 individual file for each chain.
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76
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77 -d, --distance *number*
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78 Specify distance used to extract ATOM/HETATM recods during
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79 *Distance* value of -m, --mode option. Default: *10.0* angstroms.
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80
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81 --RecordMode option controls type of record lines to extract from
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82 *PDBFile(s)*: ATOM, HETATM or both.
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83
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84 --DistanceMode *Atom | Hetatm | Residue | XYZ*
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85 Specify how to extract ATOM/HETATM records from *PDBFile(s)* during
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86 *Distance* value of -m, --mode option: extract all the records
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87 within a certain distance specifed by -d, --distance from an atom or
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88 hetro atom record, a residue, or any artbitrary point. Possible
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89 values: *Atom | Hetatm | Residue | XYZ*. Default: *XYZ*.
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90
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91 During *Residue* value of --distancemode, distance of ATOM/HETATM
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92 records is calculated from all the atoms in the residue and the
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93 records are selected as long as any atom of the residue lies with in
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94 the distace specified using -d, --distance option.
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95
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96 --RecordMode option controls type of record lines to extract from
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97 *PDBFile(s)*: ATOM, HETATM or both.
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98
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99 --DistanceSelectionMode *ByAtom | ByResidue*
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100 Specify how how to extract ATOM/HETATM records from *PDBFile(s)*
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101 during *Distance* value of -m, --mode option for all values of
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102 --DistanceMode option: extract only those ATOM/HETATM records that
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103 meet specified distance criterion; extract all records corresponding
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104 to a residue as long as one of the ATOM/HETATM record in the residue
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105 satisfies specified distance criterion. Possible values: *ByAtom,
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106 ByResidue*. Default value: *ByAtom*.
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107
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108 --DistanceOrigin *"AtomNumber,AtomName" | "HetatmNumber,HetAtmName" |
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109 "ResidueNumber,ResidueName[,ChainID]" | "X,Y,Z"*
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110 This value is --distancemode specific. In general, it identifies a
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111 point used to select other ATOM/HETATMS with in a specific distance
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112 from this point.
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113
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114 For *Atom* value of --distancemode, this option corresponds to an
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115 atom specification. Format: *AtomNumber,AtomName*. Example:
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116
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117 455,CA
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118
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119 For *Hetatm* value of --distancemode, this option corresponds to a
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120 hetatm specification. Format: *HetatmNumber,HetAtmName*. Example:
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121
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122 5295,C1
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123
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124 For *Residue* value of --distancemode, this option corresponds to a
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125 residue specification. Format: *ResidueNumber,
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126 ResidueName[,ChainID]*. Example:
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127
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128 78,MSE
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129 977,RET,A
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130 978,RET,B
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131
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132 For *XYZ* value of --distancemode, this option corresponds to a
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133 coordinate of an arbitrary point. Format: *X,Y,X*. Example:
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134
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135 10.044,19.261,-4.292
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136
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137 --RecordMode option controls type of record lines to extract from
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138 *PDBFile(s)*: ATOM, HETATM or both.
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139
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140 -h, --help
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141 Print this help message.
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142
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143 -k, --KeepOldRecords *yes | no*
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144 Specify whether to transfer old non ATOM and HETATM records from
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145 input PDBFile(s) to new PDBFile(s) during *Chains | Atoms | HetAtms
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146 | CAlphas | Distance| NonWater | NonHydrogens* value of -m --mode
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147 option. By default, except for the HEADER record, all other
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148 unnecessary non ATOM/HETATM records are dropped during the
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149 generation of new PDB files. Possible values: *yes | no*. Default:
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150 *no*.
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151
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152 -m, --mode *Chains | Sequences | Atoms | CAlphas | AtomNums | AtomsRange
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153 | AtomNames | ResidueNums | ResiduesRange | ResidueNames | Distance |
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154 NonWater | NonHydrogens*
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155 Specify what to extract from *PDBFile(s)*: *Chains* - retrieve
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156 records for specified chains; *Sequences* - generate sequence files
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157 for specific chains; *Atoms* - extract atom records; *CAlphas* -
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158 extract atom records for alpha carbon atoms; *AtomNums* - extract
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159 atom records for specified atom numbers; *AtomsRange* - extract atom
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160 records between specified atom number range; *AtomNames* - extract
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161 atom records for specified atom names; *ResidueNums* - extract
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162 records for specified residue numbers; *ResiduesRange* - extract
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163 records for residues between specified residue number range;
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164 *ResidueNames* - extract records for specified residue names;
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165 *Distance* - extract records with in a certain distance from a
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166 specific position; *NonWater* - extract records corresponding to
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167 residues other than water; *NonHydrogens* - extract non-hydrogen
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168 records.
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169
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170 Possible values: *Chains, Sequences Atoms, CAlphas, AtomNums,
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171 AtomsRange, AtomNames, ResidueNums, ResiduesRange, ResidueNames,
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172 Distance, NonWater, NonHydrogens*. Default value: *NonWater*
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173
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174 During the generation of new PDB files, unnecessay CONECT records
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175 are dropped.
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176
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177 For *Chains* mode, data for appropriate chains specified by --c
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178 --chains option is extracted from *PDBFile(s)* and placed into new
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179 PDB file(s).
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180
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181 For *Sequences* mode, residues names using various sequence related
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182 options are extracted for chains specified by --c --chains option
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183 from *PDBFile(s)* and FASTA sequence file(s) are generated.
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184
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185 For *Distance* mode, all ATOM/HETATM records with in a distance
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186 specified by -d --distance option from a specific atom, residue or a
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187 point indicated by --distancemode are extracted and placed into new
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188 PDB file(s).
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189
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190 For *NonWater* mode, non water ATOM/HETATM record lines, identified
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191 using value of --WaterResidueNames, are extracted and written to new
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192 PDB file(s).
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193
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194 For *NonHydrogens* mode, ATOM/HETATOM record lines containing
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195 element symbol other than *H* are extracted and written to new PDB
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196 file(s).
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197
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198 For all other options, appropriate ATOM/HETATM records are extracted
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199 to generate new PDB file(s).
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200
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201 --RecordMode option controls type of record lines to extract and
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202 process from *PDBFile(s)*: ATOM, HETATM or both.
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203
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204 --ModifyHeader *yes | no*
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205 Specify whether to modify HEADER record during the generation of new
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206 PDB files for -m, --mode values of *Chains | Atoms | CAlphas |
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207 Distance*. Possible values: *yes | no*. Default: *yes*. By default,
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208 Classification data is replaced by *Data extracted using
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209 MayaChemTools* before writing out HEADER record.
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210
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211 --NonStandardKeep *yes | no*
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212 Specify whether to include and convert non-standard three letter
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213 residue codes into a code specified using --nonstandardcode option
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214 and include them into sequence file(s) generated during *Sequences*
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215 value of -m, --mode option. Possible values: *yes | no*. Default:
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216 *yes*.
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217
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218 A warning is also printed about the presence of non-standard
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219 residues. Any residue other than standard 20 amino acids and 5
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220 nucleic acid is considered non-standard; additionally, HETATM
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221 residues in chains also tagged as non-standard.
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222
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223 --NonStandardCode *character*
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224 A single character code to use for non-standard residues. Default:
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225 *X*. Possible values: *?, -, or X*.
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226
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227 -o, --overwrite
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228 Overwrite existing files.
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229
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230 -r, --root *rootname*
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231 New PDB and sequence file name is generated using the root:
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232 <Root><Mode>.<Ext>. Default new file name:
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233 <PDBFileName>Chain<ChainID>.pdb for *Chains* mode;
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234 <PDBFileName>SequenceChain<ChainID>.fasta for *Sequences* mode;
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235 <PDBFileName>DistanceBy<DistanceMode>.pdb for *Distance* -m, --mode
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236 <PDBFileName><Mode>.pdb for *Atoms | CAlphas | NonWater |
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237 NonHydrogens* -m, --mode values. This option is ignored for multiple
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238 input files.
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239
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240 --RecordMode *Atom | Hetatm | AtomAndHetatm*
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241 Specify type of record lines to extract and process from
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242 *PDBFile(s)* during various values of -m, --mode option: extract
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243 only ATOM record lines; extract only HETATM record lines; extract
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244 both ATOM and HETATM lines. Possible values: *Atom | Hetatm |
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245 AtomAndHetatm | XYZ*. Default during *Atoms, CAlphas, AtomNums,
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246 AtomsRange, AtomNames* values of -m, --mode option: *Atom*;
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247 otherwise: *AtomAndHetatm*.
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248
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249 This option is ignored during *Chains, Sequences* values of -m,
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250 --mode option.
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251
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252 --Residues *"ResidueNum,[ResidueNum...]" |
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253 "StartResidueNum,EndResiduNum" | "ResidueName,[ResidueName...]"*
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254 Specify which resiude records to extract from *PDBFiles(s)* during
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255 *ResidueNums*, *ResiduesRange*,and *ResidueNames* value of -m,
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256 --mode option: extract records corresponding to residue numbers
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257 specified in a comma delimited list of residue numbers/names, or
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258 with in the range of start and end residue numbers. Possible values:
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259 *"ResidueNum[,ResidueNum,..]"*, *StartResidueNum,EndResiduNum*, or
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260 *<"ResidueName[,ResidueName,..]"*. Default: *None*. Examples:
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261
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262 20
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263 5,10
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264 TYR,SER,THR
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265
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266 --RecordMode option controls type of record lines to extract from
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267 *PDBFile(s)*: ATOM, HETATM or both.
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268
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269 --SequenceLength *number*
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270 Maximum sequence length per line in sequence file(s). Default: *80*.
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271
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272 --SequenceRecords *Atom | SeqRes*
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273 Specify which records to use for extracting residue names from
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274 *PDBFiles(s)* during *Sequences* value of -m, --mode option: use
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275 ATOM records to compile a list of residues in a chain or parse
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276 SEQRES record to get a list of residues. Possible values: *Atom |
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277 SeqRes*. Default: *Atom*.
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278
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279 --SequenceIDPrefix *FileName | HeaderRecord | Automatic*
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280 Specify how to generate a prefix for sequence IDs during *Sequences*
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281 value of -m, --mode option: use input file name prefix; retrieve PDB
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282 ID from HEADER record; or automatically decide the method for
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283 generating the prefix. The chain IDs are also appended to the
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284 prefix. Possible values: *FileName | HeaderRecord | Automatic*.
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285 Default: *Automatic*
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286
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287 --WaterResidueNames *Automatic | "ResidueName,[ResidueName,...]"*
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288 Identification of water residues during *NonWater* value of -m,
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289 --mode option. Possible values: *Automatic |
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290 "ResidueName,[ResidueName,...]"*. Default: *Automatic* - corresponds
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291 to "HOH,WAT,H20". You can also specify a different comma delimited
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292 list of residue names to use for water.
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293
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294 -w, --WorkingDir *dirname*
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295 Location of working directory. Default: current directory.
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296
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297 EXAMPLES
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298 To extract non-water records from Sample2.pdb file and generate
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299 Sample2NonWater.pdb file, type:
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300
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301 % ExtractFromPDBFiles.pl Sample2.pdb
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302
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303 To extract non-water records corresponding to only ATOM records from
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304 Sample2.pdb file and generate Sample2NonWater.pdb file, type:
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305
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306 % ExtractFromPDBFiles.pl --RecordMode Atom Sample2.pdb
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307
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308 To extract non-water records from Sample2.pdb file using HOH or WAT
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309 residue name for water along with all old non-coordinate records and
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310 generate Sample2NewNonWater.pdb file, type:
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311
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312 % ExtractFromPDBFiles.pl -m NonWater --WaterResidueNames "HOH,WAT"
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313 -KeepOldRecords Yes -r Sample2New -o Sample2.pdb
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314
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315 To extract non-hydrogens records from Sample2.pdb file and generate
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316 Sample2NonHydrogen.pdb file, type:
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317
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318 % ExtractFromPDBFiles.pl -m NonHydrogens Sample2.pdb
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319
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320 To extract data for first chain in Sample2.pdb and generate
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321 Sample2ChainA.pdb, type file, type:
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322
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323 % ExtractFromPDBFiles.pl -m chains -o Sample2.pdb
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324
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325 To extract data for both chains in Sample2.pdb and generate
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326 Sample2ChainA.pdb and Sample2ChainB.pdb, type:
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327
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328 % ExtractFromPDBFiles.pl -m chains -c All -o Sample2.pdb
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329
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330 To extract data for alpha carbons in Sample2.pdb and generate
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331 Sample2CAlphas.pdb, type:
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332
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333 % ExtractFromPDBFiles.pl -m CAlphas -o Sample2.pdb
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334
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335 To extract records for specific residue numbers in all chains from
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336 Sample2.pdb file and generate Sample2ResidueNums.pdb file, type:
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337
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338 % ExtractFromPDBFiles.pl -m ResidueNums --Residues "3,6"
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339 Sample2.pdb
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340
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341 To extract records for a specific range of residue number in all chains
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342 from Sample2.pdb file and generate Sample2ResiduesRange.pdb file, type:
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343
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344 % ExtractFromPDBFiles.pl -m ResiduesRange --Residues "10,30"
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345 Sample2.pdb
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346
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347 To extract data for all ATOM and HETATM records with in 10 angstrom of
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348 an atom specifed by atom serial number and name "1,N" in Sample2.pdb
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349 file and generate Sample2DistanceByAtom.pdb, type:
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350
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351 % ExtractFromPDBFiles.pl -m Distance --DistanceMode Atom
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352 --DistanceOrigin "1,N" -k No --distance 10 -o Sample2.pdb
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353
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354 To extract data for all ATOM and HETATM records for complete residues
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355 with any atom or hetatm less than 10 angstrom of an atom specifed by
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356 atom serial number and name "1,N" in Sample2.pdb file and generate
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357 Sample2DistanceByAtom.pdb, type:
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358
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359 % ExtractFromPDBFiles.pl -m Distance --DistanceMode Atom
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360 --DistanceOrigin "1,N" --DistanceSelectionMode ByResidue
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361 -k No --distance 10 -o Sample2.pdb
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362
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363 To extract data for all ATOM and HETATM records with in 25 angstrom of
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364 an arbitrary point "0,0,0" in Sample2.pdb file and generate
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365 Sample2DistanceByXYZ.pdb, type:
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366
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367 % ExtractFromPDBFiles.pl -m Distance --DistanceMode XYZ
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368 --DistanceOrigin "0,0,0" -k No --distance 25 -o Sample2.pdb
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369
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370 AUTHOR
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371 Manish Sud <msud@san.rr.com>
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372
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373 SEE ALSO
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374 InfoPDBFiles.pl, ModifyPDBFiles.pl
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375
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376 COPYRIGHT
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377 Copyright (C) 2015 Manish Sud. All rights reserved.
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378
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379 This file is part of MayaChemTools.
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380
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381 MayaChemTools is free software; you can redistribute it and/or modify it
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382 under the terms of the GNU Lesser General Public License as published by
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383 the Free Software Foundation; either version 3 of the License, or (at
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384 your option) any later version.
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385
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