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124 .\" ========================================================================
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125 .\"
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126 .IX Title "MODIFYPDBFILES 1"
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127 .TH MODIFYPDBFILES 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
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128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
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129 .\" way too many mistakes in technical documents.
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130 .if n .ad l
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131 .nh
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132 .SH "NAME"
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133 ModifyPDBFiles.pl \- Modify data in PDBFile(s)
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 ModifyPDBFiles.pl PDBFile(s)...
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137 .PP
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138 ModifyPDBFiles.pl [\fB\-a, \-\-AtomNumberStart\fR number] [\fB\-c, \-\-ChainIDStart\fR character]
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139 [\fB\-\-ChainIDRenameEmpty\fR yes | no] [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepOldRecords\fR yes | no]
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140 [\fB\-m, \-\-mode \fR RenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs]
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141 [\fB\-\-ModifyHeader\fR yes | no] [\fB\-o, \-\-overwrite\fR] [\fB\-\-ResidueNumberMode\fR Sequential | PerChain]
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142 [\fB\-\-ResidueNumberStart\fR number] [\fB\-\-ResidueNumberHetatmMode\fR automatic | specify]
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143 [\fB\-\-ResidueNumberStarHetatm\fR number] [\fB\-r, \-\-root\fR rootname]
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144 [\fB\-\-WaterResidueNames\fR Automatic | \*(L"ResidueName, [ResidueName,...]\*(R"] [\fB\-\-WaterResidueStart\fR number]
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145 [\fB\-w, \-\-WorkingDir\fR dirname] PDBFile(s)...
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146 .SH "DESCRIPTION"
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147 .IX Header "DESCRIPTION"
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148 Modify data in \fIPDBFile(s)\fR: renumber atoms, residues, and water residues or assign new
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149 chain IDs. Multiple PDBFile names are separated by spaces. The valid file extension is \fI.pdb\fR.
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150 All other file name extensions are ignored during the wild card expansion. All the \s-1PDB\s0 files
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151 in a current directory can be specified either by \fI*.pdb\fR or the current directory name.
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152 .SH "OPTIONS"
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153 .IX Header "OPTIONS"
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154 .IP "\fB\-a, \-\-AtomNumberStart\fR \fInumber\fR" 4
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155 .IX Item "-a, --AtomNumberStart number"
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156 Starting atom number to use during \fIRenumberAtoms\fR value of \fB\-m, \-\-mode\fR option. Default: \fI1\fR.
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157 Valid values: positive integers.
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158 .IP "\fB\-c, \-\-ChainIDStart\fR \fIcharacter\fR" 4
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159 .IX Item "-c, --ChainIDStart character"
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160 A single character to use for starting IDs for chains during \fIRenameChainIDs\fR value of \fB\-m, \-\-mode\fR option.
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161 Default: \fIA\fR. Valid values: \fIA to Z\fR.
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162 .IP "\fB\-\-ChainIDRenameEmpty\fR \fIYes | No\fR" 4
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163 .IX Item "--ChainIDRenameEmpty Yes | No"
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164 Specify whether to rename empty chain IDs during \fIRenameChainIDs\fR \fB\-m, \-\-mode\fR value. By
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165 default, \s-1ATOM\s0 and \s-1HETATM\s0 records with no chain IDs are left unchanged. Possible values:
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166 \&\fIyes | no\fR. Default: \fINo\fR.
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167 .IP "\fB\-h, \-\-help\fR" 4
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168 .IX Item "-h, --help"
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169 Print this help message.
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170 .IP "\fB\-k, \-\-KeepOldRecords\fR \fIyes | no\fR" 4
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171 .IX Item "-k, --KeepOldRecords yes | no"
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172 Specify whether to transfer old non \s-1ATOM\s0 and \s-1HETATM\s0 records from input PDBFile(s) to new
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173 PDBFile(s). By default, except for the \s-1HEADER\s0 record, all records other than \s-1ATOM/HETATM\s0
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174 are dropped during the generation of new \s-1PDB\s0 files. Possible values: \fIyes | no\fR.
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175 Default: \fIno\fR.
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176 .IP "\fB\-m, \-\-mode \fR \fIRenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs\fR" 4
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177 .IX Item "-m, --mode RenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs"
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178 Specify how to modify \fIPDBFile(s)\fR. Possible values: \fIRenumberAtoms | RenumberResidues
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179 | RenumberWaters | RenameChainIDs\fR. Default: \fIRenumberResidues\fR.
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180 .Sp
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181 For \fIRenumberAtoms\fR mode, residue number in \s-1ATOM\s0 and \s-1HETATM\s0 records are reassigned
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182 sequentially starting using value of \fB\-a, \-\-AtomNumberStart\fR option.
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183 .Sp
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184 For \fIRenumberResidues\fR mode, serial number in \s-1ATOM\s0 and \s-1HETATM\s0 records are reassigned
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185 either sequentially or statring from specified values for \s-1ATOM\s0 and \s-1HETATM\s0 records in each
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186 chain.
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187 .Sp
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188 For \fIRenumberWaters\fR mode, residue number for waters are reassigned starting from a specific
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189 value.
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190 .Sp
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191 For \fIRenameChainIDs\fR mode, all the chain IDs are reassigned starting from a specific chain \s-1ID\s0.
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192 .Sp
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193 During the generation of new \s-1PDB\s0 files, unnecessary \s-1CONECT\s0 records are dropped.
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194 .IP "\fB\-\-ModifyHeader\fR \fIyes | no\fR" 4
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195 .IX Item "--ModifyHeader yes | no"
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196 Specify whether to modify \s-1HEADER\s0 record during the generation of new \s-1PDB\s0 files
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197 Possible values: \fIyes | no\fR. Default: \fIyes\fR. By defailt, Classification data is replaced
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198 by \fIData modified using MayaChemTools\fR before writing out \s-1HEADER\s0 record.
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199 .IP "\fB\-o, \-\-overwrite\fR" 4
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200 .IX Item "-o, --overwrite"
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201 Overwrite existing files
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202 .IP "\fB\-\-ResidueNumberMode\fR \fISequential | PerChain\fR" 4
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203 .IX Item "--ResidueNumberMode Sequential | PerChain"
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204 Specify how to renumber residues: renumber residues sequentially across all the chains
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205 or start from the begining for each chain. Possible values: \fISequential | PerChain\fR. Default:
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206 \&\fIPerChain\fR.
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207 .IP "\fB\-\-ResidueNumberStart\fR \fInumber\fR" 4
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208 .IX Item "--ResidueNumberStart number"
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209 Starting residue number to use for \s-1ATOM\s0 records in chains. Default: \fI1\fR. Valid values
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210 positive integers.
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211 .Sp
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212 For \fISequential\fR value of \fB\-\-ResidueNumberMode\fR option, residue numbers are
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213 assigned sequentially across all the chains starting from the specified value.
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214 .Sp
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215 For \fIPerChain\fR value of \fB\-\-ResidueNumberMode\fR option, residue numbers are
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216 starting again from the specified value for each chain.
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217 .Sp
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218 \&\s-1HETATM\s0 residues with in the chains are numbered using this value as well
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219 .IP "\fB\-\-ResidueNumberHetatmMode\fR \fIautomatic | specify\fR" 4
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220 .IX Item "--ResidueNumberHetatmMode automatic | specify"
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221 Specify how to start residue number for \s-1HETATM\s0 records: use the next sequential
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222 residue number after the last residue number from \s-1ATOM\s0 records or start from a
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223 specific residue number. Possible values: \fIautomatic | specify\fR. Default:
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224 \&\fIautomatic\fR
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225 .Sp
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226 For \fIautomatic\fR , residue number after highest residue number of \s-1ATOM\s0
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227 records is used as the starting residue number for \s-1HETATM\s0 records.
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228 .Sp
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229 For \fIspecify\fR, value of option \fB\-\-ResidueNumberStarHetatm\fR is used as the
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230 starting residue number for \s-1HETATM\s0 records.
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231 .Sp
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232 This option along with \fB\-\-ResidueNumberStartHetatm\fR only applies to \s-1HETATM\s0 records
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233 outside the chains.
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234 .IP "\fB\-\-ResidueNumberStartHetatm\fR \fInumber\fR" 4
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235 .IX Item "--ResidueNumberStartHetatm number"
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236 Starting residue number to use for \s-1HETATM\s0 records. Default: \fI6000\fR. Valid values
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237 positive integers.
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238 .IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4
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239 .IX Item "-r, --root rootname"
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240 New \s-1PDB\s0 and sequence file name is generated using the root: <Root><Mode>.<Ext>.
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241 Default new file name: <PDBFileName><Mode>.pdb. This option is ignored for multiple
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242 input files.
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243 .ie n .IP "\fB\-\-WaterResidueNames\fR \fIAutomatic | ""ResidueName,[ResidueName,...]""\fR" 4
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244 .el .IP "\fB\-\-WaterResidueNames\fR \fIAutomatic | ``ResidueName,[ResidueName,...]''\fR" 4
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245 .IX Item "--WaterResidueNames Automatic | ResidueName,[ResidueName,...]"
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246 Identification of water residues during \fIRenumberWaters\fR value of \fB\-m, \-\-mode\fR option. Possible
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247 values: \fIAutomatic | \*(L"ResidueName,[ResidueName,...]\*(R"\fR. Default: \fIAutomatic\fR which corresponds
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248 to \*(L"\s-1HOH\s0,WAT,H20\*(R". You can also specify a different comma delimited list of residue names
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249 to use for water.
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250 .IP "\fB\-\-WaterResidueStart\fR \fInumber\fR" 4
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251 .IX Item "--WaterResidueStart number"
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252 Starting water residue number to use during \fIRenumberWaters\fR \fB\-m, \-\-mode\fR value.
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253 Default: \fI8000\fR. Valid values: positive integers.
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254 .IP "\fB\-w, \-\-WorkingDir\fR \fIdirname\fR" 4
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255 .IX Item "-w, --WorkingDir dirname"
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256 Location of working directory. Default: current directory.
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257 .SH "EXAMPLES"
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258 .IX Header "EXAMPLES"
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259 To renumber \s-1ATOM\s0 and \s-1HETATM\s0 residues starting from 1 for each chain with continuation to
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260 \&\s-1HETATM\s0 residues outside \s-1TER\s0 records in Sample2.pdb and generate
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261 Sample2RenumberResidues.pdb file, type:
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262 .PP
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263 .Vb 1
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264 \& % ModifyPDBFiles.pl Sample1.pdb
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265 .Ve
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266 .PP
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267 To renumber \s-1ATOM\s0 and \s-1HETATM\s0 residues sequentially across all chains starting from 1 with
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268 continuation to \s-1HETATM\s0 residues outside \s-1TER\s0 records in Sample2.pdb and generate
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269 Sample2RenumberResidues.pdb file, type:
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270 .PP
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271 .Vb 1
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272 \& % ModifyPDBFiles.pl \-\-ResidueNumberMode Sequential \-o Sample1.pdb
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273 .Ve
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274 .PP
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275 To renumber \s-1ATOM\s0 and \s-1HETATM\s0 residues sequentially across all chains starting from 1 and
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276 \&\s-1HETATM\s0 residues outside \s-1TER\s0 records starting from 6000 in Sample2.pdb and generate
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277 Sample2RenumberResidues.pdb file, type:
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278 .PP
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279 .Vb 2
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280 \& % ModifyPDBFiles.pl \-\-ResidueNumberMode Sequential
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281 \& \-\-ResidueNumberHetatmMode Specify \-o Sample1.pdb
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282 .Ve
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283 .PP
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284 To renumber \s-1ATOM\s0 and \s-1HETATM\s0 residues sequentially across all chains starting from 100 for
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285 \&\s-1ATOM/HETATM\s0 residues with in \s-1TER\s0 records and starting from 999 for \s-1HETATM\s0 residues
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286 outside \s-1TER\s0 records in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type:
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287 .PP
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288 .Vb 3
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289 \& % ModifyPDBFiles.pl \-\-ResidueNumberMode Sequential
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290 \& \-\-ResidueNumberHetatmMode Specify \-\-ResidueNumberStart 100
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291 \& \-\-ResidueNumberStartHetatm 999 \-o Sample2.pdb
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292 .Ve
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293 .PP
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294 To renumber \s-1ATOM\s0 and \s-1HETATM\s0 residues from 100 for each chain and starting from 999 for
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295 \&\s-1HETATM\s0 residues outside \s-1TER\s0 records in Sample2.pdb and generate Sample2RenumberResidues.pdb
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296 file, type:
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297 .PP
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298 .Vb 3
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299 \& % ModifyPDBFiles.pl \-\-ResidueNumberMode PerChain
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300 \& \-\-ResidueNumberHetatmMode Specify \-\-ResidueNumberStart 100
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301 \& \-\-ResidueNumberStartHetatm 999 \-o Sample2.pdb
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302 .Ve
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303 .PP
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304 To renumber \s-1ATOM\s0 serial numbers sequentially starting from 100 in Sample1.pdb file and generate
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305 Sample1RenumberAtoms.pdb file, type:
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306 .PP
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307 .Vb 2
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308 \& % ModifyPDBFiles.pl \-m RenumberAtoms \-\-AtomNumberStart 100
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309 \& \-o Sample1.pdb
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310 .Ve
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311 .PP
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312 To renumber water residues identified by \*(L"\s-1HOH\s0,WAT\*(R" starting from residue number 1000
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313 in Sample2.pdb file and generate Sample2RenumberWaters.pdb file, type:
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314 .PP
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315 .Vb 2
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316 \& % ModifyPDBFiles.pl \-m RenumberWaters \-\-WaterResidueNames "HOH,WAT"
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317 \& \-o \-\-WaterResidueStart 950 Sample2.pdb
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318 .Ve
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319 .PP
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320 To rename all chain IDs starting from A in Sample1.pdb file and generate
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321 Sample1RenameChainIDs.pdb file, type:
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322 .PP
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323 .Vb 1
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324 \& % ModifyPDBFiles.pl \-m RenameChainIDs \-o Sample1.pdb
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325 .Ve
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326 .PP
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327 To rename all chain IDs starting from B without assigning any chain IDs to \s-1ATOM/HETATOM\s0
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328 with no chain IDs in Sample2.pdb file and generate Sample2RenameChainIDs.pdb file, type:
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329 .PP
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330 .Vb 2
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331 \& % ModifyPDBFiles.pl l \-m RenameChainIDs \-c B \-\-ChainIDRenameEmpty No
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332 \& \-o Sample2.pdb
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333 .Ve
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334 .SH "AUTHOR"
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335 .IX Header "AUTHOR"
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336 Manish Sud <msud@san.rr.com>
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337 .SH "SEE ALSO"
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338 .IX Header "SEE ALSO"
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339 ExtractFromPDBFiles.pl, InfoPDBFiles.pl
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340 .SH "COPYRIGHT"
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341 .IX Header "COPYRIGHT"
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342 Copyright (C) 2015 Manish Sud. All rights reserved.
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343 .PP
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344 This file is part of MayaChemTools.
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345 .PP
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346 MayaChemTools is free software; you can redistribute it and/or modify it under
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347 the terms of the \s-1GNU\s0 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.
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