processDCD.pl

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