MMTSB
Tool Set Documentation

Difference between revisions of "processDCD.pl"

From MMTSB
Jump to: navigation, search
Line 11: Line 11:
  
 
; -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 :  
 
; -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 :

Revision as of 04:55, 29 July 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 trajectory file with custom commands and custom functions.

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 
-apply cmd 
each frame will be temporarily converted into a PDB file and analyzed according to the given command
-function file 
-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 
-boxsize 
-average 
-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