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 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