MMTSB
Tool Set Documentation

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:to : analyze the specified frame range from trajectory file
+
; -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 :
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; -qscore ref : calculate Q-score for each frame
; -boxsize :  
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; -boxsize : extract box size information from trajectory
; -average :  
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; -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:to : use specified atom selection range
+
; -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]

Show source


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