view mayachemtools/docs/scripts/man1/ExtractFromPDBFiles.1 @ 2:dfff2614510e draft

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.\" ========================================================================
.\"
.IX Title "EXTRACTFROMPDBFILES 1"
.TH EXTRACTFROMPDBFILES 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
ExtractFromPDBFiles.pl \- Extract specific data from PDBFile(s)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
ExtractFromPDBFiles.pl PDBFile(s)...
.PP
ExtractFromPDBFiles.pl [\fB\-a, \-\-Atoms\fR \*(L"AtomNum, [AtomNum...]\*(R" | \*(L"StartAtomNum, EndAtomNum\*(R" |
\&\*(L"AtomName, [AtomName...]\*(R"] [\fB\-c, \-\-chains\fR First | All | \*(L"ChainID, [ChainID,...]\*(R"]
[<\-\-CombineChains> yes | no] [\fB\-d, \-\-distance\fR number] [\fB\-\-DistanceMode\fR Atom | Hetatm | Residue | \s-1XYZ\s0]
[\fB\-\-DistanceOrigin\fR \*(L"AtomNumber, AtomName\*(R" | \*(L"HetatmNumber, HetAtmName\*(R" | \*(L"ResidueNumber, ResidueName, [ChainID]\*(R" | \*(L"X,Y,Z\*(R">]
[<\-\-DistanceSelectionMode> ByAtom | ByResidue] [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepOldRecords\fR yes | no]
[\fB\-m, \-\-mode \fR Chains | Sequences | Atoms | CAlphas | AtomNums | AtomsRange | AtomNames |
ResidueNums | ResiduesRange | ResidueNames | Distance | NonWater | NonHydrogens]
[\fB\-\-ModifyHeader\fR yes | no] [\fB\-\-NonStandardKeep\fR yes | no] [\fB\-\-NonStandardCode\fR character]
[\fB\-o, \-\-overwrite\fR] [\fB\-r, \-\-root\fR rootname] \fB\-\-RecordMode\fR \fIAtom | Hetatm | AtomAndHetatm\fR]
[\fB\-\-Residues\fR \*(L"ResidueNum,[ResidueNum...]\*(R" | StartResidueNum,EndResiduNum ]
[\fB\-\-SequenceLength\fR number] [\fB\-\-SequenceRecords\fR Atom | SeqRes]
[\fB\-\-SequenceIDPrefix\fR FileName | HeaderRecord | Automatic]
[\fB\-\-WaterResidueNames\fR Automatic | \*(L"ResidueName, [ResidueName,...]\*(R"]
[\fB\-w, \-\-WorkingDir\fR dirname] PDBFile(s)...
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Extract specific data from \fIPDBFile(s)\fR and generate appropriate \s-1PDB\s0 or sequence file(s).
Multiple PDBFile names are separated by spaces. The valid file extension is \fI.pdb\fR.
All other file name extensions are ignored during the wild card expansion. All the \s-1PDB\s0 files
in a current directory can be specified either by \fI*.pdb\fR or the current directory name.
.PP
During \fIChains\fR and \fISequences\fR values of \fB\-m, \-\-mode\fR option, all \s-1ATOM/HETAM\s0 records
for chains after the first model in \s-1PDB\s0 fils containing data for multiple models are ignored.
.SH "OPTIONS"
.IX Header "OPTIONS"
.ie n .IP "\fB\-a, \-\-Atoms\fR \fI""AtomNum,[AtomNum...]"" | ""StartAtomNum,EndAtomNum"" | ""AtomName,[AtomName...]""\fR" 4
.el .IP "\fB\-a, \-\-Atoms\fR \fI``AtomNum,[AtomNum...]'' | ``StartAtomNum,EndAtomNum'' | ``AtomName,[AtomName...]''\fR" 4
.IX Item "-a, --Atoms AtomNum,[AtomNum...] | StartAtomNum,EndAtomNum | AtomName,[AtomName...]"
Specify which atom records to extract from \fIPDBFiles(s)\fR during \fIAtomNums\fR,
\&\fIAtomsRange\fR, and \fIAtomNames\fR value of \fB\-m, \-\-mode\fR option: extract records
corresponding to atom numbers specified in a comma delimited list of atom numbers/names,
or with in the range of start and end atom numbers. Possible values: \fI\*(L"AtomNum[,AtomNum,..]\*(R"\fR,
\&\fIStartAtomNum,EndAtomNum\fR, or \fI\*(L"AtomName[,AtomName,..]\*(R"\fR. Default: \fINone\fR. Examples:
.Sp
.Vb 3
\&    10
\&    15,20
\&    N,CA,C,O
.Ve
.IP "\fB\-c, \-\-chains\fR \fIFirst | All | ChainID,[ChainID,...]\fR" 4
.IX Item "-c, --chains First | All | ChainID,[ChainID,...]"
Specify which chains to extract from \fIPDBFile(s)\fR during \fIChains | Sequences\fR value of
\&\fB\-m, \-\-mode\fR option: first chain, all chains, or a specific list of comma delimited chain IDs.
Possible values: \fIFirst | All | ChainID,[ChainID,...]\fR. Default: \fIFirst\fR. Examples:
.Sp
.Vb 3
\&    A
\&    A,B
\&    All
.Ve
.IP "\fB\-\-CombineChains\fR \fIyes | no\fR" 4
.IX Item "--CombineChains yes | no"
Specify whether to combine extracted chains data into a single file during \fIChains\fR or
\&\fISequences\fR value of \fB\-m, \-\-mode\fR option. Possible values: \fIyes | no\fR. Default: \fIno\fR.
.Sp
During \fIChains\fR value of <\-m, \-\-mode> option with \fIYes\fR value of <\-\-CombineChains>,
extracted data for specified chains is written into a single file instead of individual file for each
chain.
.Sp
During \fISequences\fR value of <\-m, \-\-mode> option with \fIYes\fR value of <\-\-CombineChains>,
residues sequences for specified chains are extracted and concatenated into a single sequence
file instead of  individual file for each chain.
.IP "\fB\-d, \-\-distance\fR \fInumber\fR" 4
.IX Item "-d, --distance number"
Specify distance used to extract \s-1ATOM/HETATM\s0 recods during \fIDistance\fR value of
\&\fB\-m, \-\-mode\fR option. Default: \fI10.0\fR angstroms.
.Sp
\&\fB\-\-RecordMode\fR option controls type of record lines to extract from \fIPDBFile(s)\fR:
\&\s-1ATOM\s0, \s-1HETATM\s0 or both.
.IP "\fB\-\-DistanceMode\fR \fIAtom | Hetatm | Residue | \s-1XYZ\s0\fR" 4
.IX Item "--DistanceMode Atom | Hetatm | Residue | XYZ"
Specify how to extract \s-1ATOM/HETATM\s0 records from \fIPDBFile(s)\fR during \fIDistance\fR value of
\&\fB\-m, \-\-mode\fR option: extract all the records within a certain distance specifed by \fB\-d, \-\-distance\fR
from an atom or hetro atom record, a residue, or any artbitrary point. Possible values: \fIAtom |
Hetatm | Residue | \s-1XYZ\s0\fR. Default: \fI\s-1XYZ\s0\fR.
.Sp
During \fIResidue\fR value of \fB\-\-distancemode\fR, distance of \s-1ATOM/HETATM\s0 records is calculated from
all the atoms in the residue and the records are selected as long as any atom of the residue lies with
in the distace specified using \fB\-d, \-\-distance\fR option.
.Sp
\&\fB\-\-RecordMode\fR option controls type of record lines to extract from \fIPDBFile(s)\fR:
\&\s-1ATOM\s0, \s-1HETATM\s0 or both.
.IP "\fB\-\-DistanceSelectionMode\fR \fIByAtom | ByResidue\fR" 4
.IX Item "--DistanceSelectionMode ByAtom | ByResidue"
Specify how how to extract \s-1ATOM/HETATM\s0 records from \fIPDBFile(s)\fR during \fIDistance\fR value of
\&\fB\-m, \-\-mode\fR option for all values of \fB\-\-DistanceMode\fR option: extract only those \s-1ATOM/HETATM\s0
records that meet specified distance criterion; extract all records corresponding to a residue as
long as one of the \s-1ATOM/HETATM\s0 record in the residue satisfies specified distance criterion. Possible
values: \fIByAtom, ByResidue\fR. Default value: \fIByAtom\fR.
.ie n .IP "\fB\-\-DistanceOrigin\fR \fI""AtomNumber,AtomName"" | ""HetatmNumber,HetAtmName"" | ""ResidueNumber,ResidueName[,ChainID]"" | ""X,Y,Z""\fR" 4
.el .IP "\fB\-\-DistanceOrigin\fR \fI``AtomNumber,AtomName'' | ``HetatmNumber,HetAtmName'' | ``ResidueNumber,ResidueName[,ChainID]'' | ``X,Y,Z''\fR" 4
.IX Item "--DistanceOrigin AtomNumber,AtomName | HetatmNumber,HetAtmName | ResidueNumber,ResidueName[,ChainID] | X,Y,Z"
This value is \fB\-\-distancemode\fR specific. In general, it identifies a point used to select
other \s-1ATOM/HETATMS\s0 with in a specific distance from this point.
.Sp
For \fIAtom\fR value of \fB\-\-distancemode\fR, this option corresponds to an atom specification.
Format: \fIAtomNumber,AtomName\fR. Example:
.Sp
.Vb 1
\&    455,CA
.Ve
.Sp
For \fIHetatm\fR value of \fB\-\-distancemode\fR, this option corresponds to a hetatm specification.
Format: \fIHetatmNumber,HetAtmName\fR. Example:
.Sp
.Vb 1
\&    5295,C1
.Ve
.Sp
For \fIResidue\fR value of \fB\-\-distancemode\fR, this option corresponds to a residue specification.
Format: \fIResidueNumber, ResidueName[,ChainID]\fR. Example:
.Sp
.Vb 3
\&    78,MSE
\&    977,RET,A
\&    978,RET,B
.Ve
.Sp
For \fI\s-1XYZ\s0\fR value of \fB\-\-distancemode\fR, this option corresponds to a coordinate of an
arbitrary point. Format: \fIX,Y,X\fR. Example:
.Sp
.Vb 1
\&    10.044,19.261,\-4.292
.Ve
.Sp
\&\fB\-\-RecordMode\fR option controls type of record lines to extract from \fIPDBFile(s)\fR:
\&\s-1ATOM\s0, \s-1HETATM\s0 or both.
.IP "\fB\-h, \-\-help\fR" 4
.IX Item "-h, --help"
Print this help message.
.IP "\fB\-k, \-\-KeepOldRecords\fR \fIyes | no\fR" 4
.IX Item "-k, --KeepOldRecords yes | no"
Specify whether to transfer old non \s-1ATOM\s0 and \s-1HETATM\s0 records from input PDBFile(s) to new
PDBFile(s) during \fIChains | Atoms | HetAtms | CAlphas | Distance| NonWater | NonHydrogens\fR
value of \fB\-m \-\-mode\fR option. By default, except for the \s-1HEADER\s0 record, all
other unnecessary non \s-1ATOM/HETATM\s0 records are dropped during the
generation of new \s-1PDB\s0 files. Possible values: \fIyes | no\fR. Default: \fIno\fR.
.IP "\fB\-m, \-\-mode \fR \fIChains | Sequences | Atoms | CAlphas | AtomNums | AtomsRange | AtomNames | ResidueNums | ResiduesRange | ResidueNames | Distance | NonWater | NonHydrogens\fR" 4
.IX Item "-m, --mode  Chains | Sequences | Atoms | CAlphas | AtomNums | AtomsRange | AtomNames | ResidueNums | ResiduesRange | ResidueNames | Distance | NonWater | NonHydrogens"
Specify what to extract from \fIPDBFile(s)\fR: \fIChains\fR \- retrieve records for
specified chains; \fISequences\fR \- generate sequence files for specific chains;
\&\fIAtoms\fR \- extract atom records; \fICAlphas\fR \- extract atom records for alpha
carbon atoms; \fIAtomNums\fR \- extract atom records for specified atom numbers;
\&\fIAtomsRange\fR \- extract atom records between specified atom number range;
\&\fIAtomNames\fR \- extract atom records for specified atom names; \fIResidueNums\fR
\&\- extract records for specified residue numbers; \fIResiduesRange\fR \- extract records
for residues between specified residue number range; \fIResidueNames\fR \- extract
records for specified residue names; \fIDistance\fR \- extract records with in a
certain distance from a specific position; \fINonWater\fR \- extract records corresponding
to residues other than water; \fINonHydrogens\fR \- extract non-hydrogen records.
.Sp
Possible values: \fIChains, Sequences Atoms, CAlphas, AtomNums, AtomsRange,
AtomNames, ResidueNums, ResiduesRange, ResidueNames, Distance, NonWater,
NonHydrogens\fR. Default value: \fINonWater\fR
.Sp
During the generation of new \s-1PDB\s0 files, unnecessay \s-1CONECT\s0 records are dropped.
.Sp
For \fIChains\fR mode, data for appropriate chains specified by \fB\-\-c \-\-chains\fR option
is extracted from \fIPDBFile(s)\fR and placed into new \s-1PDB\s0 file(s).
.Sp
For \fISequences\fR mode, residues names using various sequence related options are
extracted for chains specified by \fB\-\-c \-\-chains\fR option from \fIPDBFile(s)\fR and
\&\s-1FASTA\s0 sequence file(s) are generated.
.Sp
For \fIDistance\fR mode, all \s-1ATOM/HETATM\s0 records with in a distance specified
by \fB\-d \-\-distance\fR option from a specific atom, residue or a point indicated by
\&\fB\-\-distancemode\fR are extracted and placed into new \s-1PDB\s0 file(s).
.Sp
For \fINonWater\fR mode, non water \s-1ATOM/HETATM\s0 record lines, identified using value of
\&\fB\-\-WaterResidueNames\fR, are extracted and written to new \s-1PDB\s0 file(s).
.Sp
For \fINonHydrogens\fR mode, \s-1ATOM/HETATOM\s0 record lines containing element symbol
other than \fIH\fR are extracted and written to new \s-1PDB\s0 file(s).
.Sp
For all other options, appropriate \s-1ATOM/HETATM\s0 records are extracted to generate new
\&\s-1PDB\s0 file(s).
.Sp
\&\fB\-\-RecordMode\fR option controls type of record lines to extract and process from
\&\fIPDBFile(s)\fR: \s-1ATOM\s0, \s-1HETATM\s0 or both.
.IP "\fB\-\-ModifyHeader\fR \fIyes | no\fR" 4
.IX Item "--ModifyHeader yes | no"
Specify whether to modify \s-1HEADER\s0 record during the generation of new \s-1PDB\s0 files
for \fB\-m, \-\-mode\fR values of \fIChains | Atoms | CAlphas | Distance\fR. Possible values:
\&\fIyes | no\fR.  Default: \fIyes\fR. By default, Classification data is replaced by \fIData extracted
using MayaChemTools\fR before writing out \s-1HEADER\s0 record.
.IP "\fB\-\-NonStandardKeep\fR \fIyes | no\fR" 4
.IX Item "--NonStandardKeep yes | no"
Specify whether to include and convert non-standard three letter residue codes into
a code specified using \fB\-\-nonstandardcode\fR option and include them into sequence file(s)
generated during \fISequences\fR value of \fB\-m, \-\-mode\fR option. Possible values: \fIyes | no\fR.
Default: \fIyes\fR.
.Sp
A warning is also printed about the presence of non-standard residues. Any residue other
than standard 20 amino acids and 5 nucleic acid is considered non-standard; additionally,
\&\s-1HETATM\s0 residues in chains also tagged as non-standard.
.IP "\fB\-\-NonStandardCode\fR \fIcharacter\fR" 4
.IX Item "--NonStandardCode character"
A single character code to use for non-standard residues. Default: \fIX\fR. Possible values:
\&\fI?, \-, or X\fR.
.IP "\fB\-o, \-\-overwrite\fR" 4
.IX Item "-o, --overwrite"
Overwrite existing files.
.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4
.IX Item "-r, --root rootname"
New \s-1PDB\s0 and sequence file name is generated using the root: <Root><Mode>.<Ext>.
Default new file name: <PDBFileName>Chain<ChainID>.pdb for \fIChains\fR \fBmode\fR;
<PDBFileName>SequenceChain<ChainID>.fasta for \fISequences\fR \fBmode\fR;
<PDBFileName>DistanceBy<DistanceMode>.pdb for \fIDistance\fR \fB\-m, \-\-mode\fR
<PDBFileName><Mode>.pdb for \fIAtoms | CAlphas | NonWater | NonHydrogens\fR \fB\-m, \-\-mode\fR
values. This option is ignored for multiple input files.
.IP "\fB\-\-RecordMode\fR \fIAtom | Hetatm | AtomAndHetatm\fR" 4
.IX Item "--RecordMode Atom | Hetatm | AtomAndHetatm"
Specify type of record lines to extract and process from \fIPDBFile(s)\fR during various
values of \fB\-m, \-\-mode\fR option: extract only \s-1ATOM\s0 record lines; extract only \s-1HETATM\s0
record lines; extract both \s-1ATOM\s0 and \s-1HETATM\s0 lines. Possible values: \fIAtom | Hetatm
| AtomAndHetatm | \s-1XYZ\s0\fR. Default during \fIAtoms, CAlphas, AtomNums, AtomsRange,
AtomNames\fR values of \fB\-m, \-\-mode\fR option: \fIAtom\fR; otherwise: \fIAtomAndHetatm\fR.
.Sp
This option is ignored during \fIChains, Sequences\fR values of \fB\-m, \-\-mode\fR option.
.ie n .IP "\fB\-\-Residues\fR \fI""ResidueNum,[ResidueNum...]"" | ""StartResidueNum,EndResiduNum"" | ""ResidueName,[ResidueName...]""\fR" 4
.el .IP "\fB\-\-Residues\fR \fI``ResidueNum,[ResidueNum...]'' | ``StartResidueNum,EndResiduNum'' | ``ResidueName,[ResidueName...]''\fR" 4
.IX Item "--Residues ResidueNum,[ResidueNum...] | StartResidueNum,EndResiduNum | ResidueName,[ResidueName...]"
Specify which resiude records to extract from \fIPDBFiles(s)\fR during \fIResidueNums\fR,
\&\fIResiduesRange\fR,and \fIResidueNames\fR value of \fB\-m, \-\-mode\fR option: extract records
corresponding to residue numbers specified in a comma delimited list of residue numbers/names,
or with in the range of start and end residue numbers. Possible values: \fI\*(L"ResidueNum[,ResidueNum,..]\*(R"\fR,
\&\fIStartResidueNum,EndResiduNum\fR, or \fI<\*(L"ResidueName[,ResidueName,..]\*(R"\fR. Default: \fINone\fR. Examples:
.Sp
.Vb 3
\&    20
\&    5,10
\&    TYR,SER,THR
.Ve
.Sp
\&\fB\-\-RecordMode\fR option controls type of record lines to extract from \fIPDBFile(s)\fR:
\&\s-1ATOM\s0, \s-1HETATM\s0 or both.
.IP "\fB\-\-SequenceLength\fR \fInumber\fR" 4
.IX Item "--SequenceLength number"
Maximum sequence length per line in sequence file(s). Default: \fI80\fR.
.IP "\fB\-\-SequenceRecords\fR \fIAtom | SeqRes\fR" 4
.IX Item "--SequenceRecords Atom | SeqRes"
Specify which records to use for extracting residue names from \fIPDBFiles(s)\fR during
\&\fISequences\fR value of \fB\-m, \-\-mode\fR option: use \s-1ATOM\s0 records to compile a list
of residues in a chain or parse \s-1SEQRES\s0 record to get a list of residues. Possible values:
\&\fIAtom | SeqRes\fR. Default: \fIAtom\fR.
.IP "\fB\-\-SequenceIDPrefix\fR \fIFileName | HeaderRecord | Automatic\fR" 4
.IX Item "--SequenceIDPrefix FileName | HeaderRecord | Automatic"
Specify how to generate a prefix for sequence IDs during \fISequences\fR value
of \fB\-m, \-\-mode\fR option: use input file name prefix; retrieve \s-1PDB\s0 \s-1ID\s0 from \s-1HEADER\s0 record;
or automatically decide the method for generating the prefix. The chain IDs are also
appended to the prefix. Possible values: \fIFileName | HeaderRecord | Automatic\fR.
Default: \fIAutomatic\fR
.ie n .IP "\fB\-\-WaterResidueNames\fR \fIAutomatic | ""ResidueName,[ResidueName,...]""\fR" 4
.el .IP "\fB\-\-WaterResidueNames\fR \fIAutomatic | ``ResidueName,[ResidueName,...]''\fR" 4
.IX Item "--WaterResidueNames Automatic | ResidueName,[ResidueName,...]"
Identification of water residues during \fINonWater\fR value of \fB\-m, \-\-mode\fR option. Possible values:
\&\fIAutomatic | \*(L"ResidueName,[ResidueName,...]\*(R"\fR. Default: \fIAutomatic\fR \- corresponds
to \*(L"\s-1HOH\s0,WAT,H20\*(R". You can also specify a different comma delimited list of residue names
to use for water.
.IP "\fB\-w, \-\-WorkingDir\fR \fIdirname\fR" 4
.IX Item "-w, --WorkingDir dirname"
Location of working directory. Default: current directory.
.SH "EXAMPLES"
.IX Header "EXAMPLES"
To extract non-water records from Sample2.pdb file and generate Sample2NonWater.pdb
file, type:
.PP
.Vb 1
\&    % ExtractFromPDBFiles.pl Sample2.pdb
.Ve
.PP
To extract non-water records corresponding to only \s-1ATOM\s0 records from Sample2.pdb file
and generate Sample2NonWater.pdb file, type:
.PP
.Vb 1
\&    % ExtractFromPDBFiles.pl \-\-RecordMode Atom Sample2.pdb
.Ve
.PP
To extract non-water records from Sample2.pdb file using \s-1HOH\s0 or \s-1WAT\s0 residue name for water along
with all old non-coordinate records and generate Sample2NewNonWater.pdb file, type:
.PP
.Vb 2
\&    % ExtractFromPDBFiles.pl \-m NonWater \-\-WaterResidueNames "HOH,WAT"
\&      \-KeepOldRecords Yes \-r Sample2New \-o Sample2.pdb
.Ve
.PP
To extract non-hydrogens records from Sample2.pdb file and generate Sample2NonHydrogen.pdb
file, type:
.PP
.Vb 1
\&    % ExtractFromPDBFiles.pl \-m NonHydrogens Sample2.pdb
.Ve
.PP
To extract data for first chain in Sample2.pdb and generate Sample2ChainA.pdb, type
file, type:
.PP
.Vb 1
\&    % ExtractFromPDBFiles.pl \-m chains \-o Sample2.pdb
.Ve
.PP
To extract data for both chains in Sample2.pdb and generate Sample2ChainA.pdb and
Sample2ChainB.pdb, type:
.PP
.Vb 1
\&    % ExtractFromPDBFiles.pl \-m chains \-c All \-o Sample2.pdb
.Ve
.PP
To extract data for alpha carbons in Sample2.pdb and generate Sample2CAlphas.pdb, type:
.PP
.Vb 1
\&    % ExtractFromPDBFiles.pl \-m CAlphas \-o Sample2.pdb
.Ve
.PP
To extract records for specific residue numbers in all chains from Sample2.pdb file and generate
Sample2ResidueNums.pdb file, type:
.PP
.Vb 2
\&    % ExtractFromPDBFiles.pl \-m ResidueNums \-\-Residues "3,6"
\&      Sample2.pdb
.Ve
.PP
To extract records for a specific range of residue number in all chains from Sample2.pdb
file and generate Sample2ResiduesRange.pdb file, type:
.PP
.Vb 2
\&    % ExtractFromPDBFiles.pl \-m ResiduesRange \-\-Residues "10,30"
\&      Sample2.pdb
.Ve
.PP
To extract data for all \s-1ATOM\s0 and \s-1HETATM\s0 records with in 10 angstrom of an atom specifed by
atom serial number and name \*(L"1,N\*(R" in Sample2.pdb file and generate Sample2DistanceByAtom.pdb,
type:
.PP
.Vb 2
\&    % ExtractFromPDBFiles.pl \-m Distance \-\-DistanceMode Atom
\&      \-\-DistanceOrigin "1,N" \-k No \-\-distance 10 \-o Sample2.pdb
.Ve
.PP
To extract data for all \s-1ATOM\s0 and \s-1HETATM\s0 records for complete residues with any atom or hetatm
less than 10 angstrom of an atom specifed by atom serial number and name \*(L"1,N\*(R" in Sample2.pdb
file and generate Sample2DistanceByAtom.pdb, type:
.PP
.Vb 3
\&    % ExtractFromPDBFiles.pl \-m Distance \-\-DistanceMode Atom
\&      \-\-DistanceOrigin "1,N" \-\-DistanceSelectionMode ByResidue
\&      \-k No \-\-distance 10 \-o Sample2.pdb
.Ve
.PP
To extract data for all \s-1ATOM\s0 and \s-1HETATM\s0 records with in 25 angstrom of an arbitrary point \*(L"0,0,0\*(R"
in Sample2.pdb file and generate Sample2DistanceByXYZ.pdb, type:
.PP
.Vb 2
\&    % ExtractFromPDBFiles.pl \-m Distance \-\-DistanceMode XYZ
\&      \-\-DistanceOrigin "0,0,0" \-k No \-\-distance 25 \-o Sample2.pdb
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
InfoPDBFiles.pl, ModifyPDBFiles.pl
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
Copyright (C) 2015 Manish Sud. All rights reserved.
.PP
This file is part of MayaChemTools.
.PP
MayaChemTools is free software; you can redistribute it and/or modify it under
the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option)
any later version.