MMTSB
Tool Set Documentation

dihed.pl

From MMTSB
Revision as of 14:09, 12 August 2006 by Feig (talk | contribs)
(diff) ←Older revision | view current revision (diff) | Newer revision→ (diff)
Jump to: navigation, search

Usage

usage:   dihed.pl [options] [refPDB [cmpPDB]]
options: [-l min:max[...]]
         [-list phi|psi|chi1|chi2|chi3|chi4|chi5|omega]
         [-atoms [chain]res:name [chain]res:name [chain]res:name [chain]res:name

Show source


Description

This script calculates phi, psi, and chi1 dihedral angles. If two structures are given as input it calculates the root mean square deviation for all residues as well as the fraction of angles in the second structure found within 40 degrees of the corresponding angle in the reference structure.
With the option -list followed by phi, psi, omega, or chi1 and a single structure as argument a list of dihedral angles is written to standard output.
The option -l is available to restricts the comparison or list output to a residue subset.

Options

-help 
usage information


Examples

dihed.pl 1vii.exp.pdb 1vii.exp.min.pdb
calculates phi, psi, and chi1 dihedral deviations

phi: 33.270 ( 85.71 % ), psi: 41.244 ( 77.14 % ), chi1: 36.318 ( 70.97 % )


dihed.pl -list phi 1vii.exp.pdb
lists phi dihedral angles for all residues in the given protein structure

MET1:    0.000
LEU2:  -64.308
SER3:  -63.139
ASP4:  -33.485
GLU5:  -36.210
ASP6:  -47.252
PHE7:  -42.580
LYS8:  -35.823
ALA9:  -79.382
VAL10: -140.773

...


dihed.pl -l 10:21 1vii.exp.pdb 1vii.exp.min.pdb
compares dihedral angles only for residues 10 through 21

phi: 30.428 ( 75.00 % ), psi: 37.130 ( 75.00 % ), chi1: 34.822 ( 66.67 % )