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Difference between revisions of "processDCD.pl"
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== Description == | == Description == | ||
| − | Process a trajectory file with custom commands and custom functions. | + | Process a CHARMM trajectory file with custom commands and custom functions. |
| + | This function provides similar function to [[analyzeCHARMM.pl]] but does not require CHARMM and offers greater flexibility, especially for non-standard | ||
| + | systems. | ||
== Options == | == Options == | ||
; -help : usage information | ; -help : usage information | ||
| − | ; -inx from | + | ; -inx from:to : analyze the specified frame range from trajectory file |
; -step size : skip the specified number of steps in between frame analyses | ; -step size : skip the specified number of steps in between frame analyses | ||
| − | ; -multi from:to | + | ; -multi from:to : read from multiple DCD files (file name given as template) with indices according to given range of numbers |
; -apply cmd : each frame will be temporarily converted into a PDB file and analyzed according to the given command | ; -apply cmd : each frame will be temporarily converted into a PDB file and analyzed according to the given command | ||
| − | ; -function file : | + | ; -function file : analyze frames with an internal perl function (see [[analyze.pl]] for more information |
; -extract name : extract structures and store them as PDB files with a common tag name | ; -extract name : extract structures and store them as PDB files with a common tag name | ||
; -ensdir dir : extract structures into an ensemble with the specified directory name | ; -ensdir dir : extract structures into an ensemble with the specified directory name | ||
; -ens tag : extract structures into an ensemble with the specified tag name | ; -ens tag : extract structures into an ensemble with the specified tag name | ||
; -rms CA|CAB|C|O|N|side|back|all ... ref : calculate the root mean square deviation of each frame with respect to a reference PDB structure | ; -rms CA|CAB|C|O|N|side|back|all ... ref : calculate the root mean square deviation of each frame with respect to a reference PDB structure | ||
| − | ; -qscore ref : | + | ; -qscore ref : calculate Q-score for each frame |
| − | ; -boxsize : | + | ; -boxsize : extract box size information from trajectory |
| − | ; -average : | + | ; -average : calculate average structure from trajectory |
; -fit ref : fit each frame to the reference | ; -fit ref : fit each frame to the reference | ||
; -fitsel cab|ca|cb|heavy : fit each frame with respect to the specified atom selection | ; -fitsel cab|ca|cb|heavy : fit each frame with respect to the specified atom selection | ||
; -psf file : use specified protein structure file (PSF) | ; -psf file : use specified protein structure file (PSF) | ||
| − | ; -atoms from | + | ; -atoms from:to : use specified atom selection range |
== Examples == | == Examples == | ||
| + | |||
| + | <mmtsbToolExample cmd="processDCD.pl" set="test1"></mmtsbToolExample> | ||
Latest revision as of 01:21, 1 August 2009
Usage
usage: processDCD.pl [template] [dcdfile(s)]
options: [-inx index[:to]] [-step n]
[-multi from:to]
[-apply cmd]
[-function file]
[-extract name]
[-ensdir dir] [-ens tag]
[-rms CA|CAB|C|O|N|side|back|all ref] [-useseg]
[-rmsl min:max[...]]
[-qscore ref] [-boxsize]
[-wrapseg]
[-average] [-fit] [-fitsel cab|ca|cb|heavy] [-fitresnumonly]
[-fitl min:max[...]]
[-ref ref]
[-psf file]
[-tag value]
Description
Process a CHARMM trajectory file with custom commands and custom functions. This function provides similar function to analyzeCHARMM.pl but does not require CHARMM and offers greater flexibility, especially for non-standard systems.
Options
- -help
- usage information
- -inx from:to
- analyze the specified frame range from trajectory file
- -step size
- skip the specified number of steps in between frame analyses
- -multi from:to
- read from multiple DCD files (file name given as template) with indices according to given range of numbers
- -apply cmd
- each frame will be temporarily converted into a PDB file and analyzed according to the given command
- -function file
- analyze frames with an internal perl function (see analyze.pl for more information
- -extract name
- extract structures and store them as PDB files with a common tag name
- -ensdir dir
- extract structures into an ensemble with the specified directory name
- -ens tag
- extract structures into an ensemble with the specified tag name
- -rms CA|CAB|C|O|N|side|back|all ... ref
- calculate the root mean square deviation of each frame with respect to a reference PDB structure
- -qscore ref
- calculate Q-score for each frame
- -boxsize
- extract box size information from trajectory
- -average
- calculate average structure from trajectory
- -fit ref
- fit each frame to the reference
- -fitsel cab|ca|cb|heavy
- fit each frame with respect to the specified atom selection
- -psf file
- use specified protein structure file (PSF)
- -atoms from:to
- use specified atom selection range
Examples
processDCD.pl -inx 5:10 -apply rgyr.pl 1vii.pdb 1vii.dcd
calculates the radius of gyration for structures from frames 5-10 from this trajectory
reading from 1vii.dcd 5 5.0000 12.303517 6 6.0000 9.622869 7 7.0000 9.159078 8 8.0000 9.735043 9 9.0000 9.278946 10 10.0000 9.796450