PhiPsi_restraints (Supplementary backbone torsion angle restraints for CNS).¶
Section author: Michael S. Chapman <chapmami@ohsu.edu>
Module author: Michael S. Chapman <chapmami@ohsu.edu>
| Authors: | Michael S. Chapman <chapmami@ohsu.edu>, Oregon Health & Science University |
|---|---|
| Version: | 0.5, March 23, 2016 |
| usage: | phipsi_restraints.py [-h] -t <phi_min, phi_max, psi_min, psi_max> -n <name> [-t <phi_min, phi_max, psi_min, psi_max> -n <name> ...] -g <phi_min, phi_max, psi_min, psi_max> -N <name> [-g <phi_min, phi_max, psi_min, psi_max> -N <name> ...] [-G ] <input-pdb-file> <output-file> where <output-file> is a CNS additional restraints file that can be edited. |
Changed in version 0.1: 08/19/11
Changed in version 0.2: 11/25/12 Use PDB file directly instead of MoleMan phipsi output.
Changed in version 0.5: 05/20/2015 ReStructuredText docs
Synopsis¶
Generates a text file of CNS supplementary retraints to penalize variation of backbone torsion angles outside user-defined (φ, ψ) regions of a Ramachandran plot.
Usage¶
Using command-line arguments, the user defines square regions on the Ramachandran plot that are allowable. These might correspond to the α and β regions that are commonly marked as favorable on a Ramachandran plot. Non-square areas are supported by the user supplying multiple overlapping boxes, with residues allowed to have (φ, ψ) in any of the boxes (logical OR).
Optionally, the user can provide separate box definitions for glycine residues, and dictate whether these are to be expanded centrosymmetrically to account for the increased (φ, ψ) combinations allowed. (Distinctions between other types of residues are not supported.)
The output text file can be read as commands of supplementary restraints by a CNS job. Typically, one would want to edit the top of the file to adjust the weighting.
Command-line options¶
The most up-to-date documentation is generated from python -u -m cns.phipsi_restraints -h:
Example:¶
The following bash scrhipr will restrain to an approximation of the favored areas of a Ramachandran plot, giving glycines more fredom:
#!/bin/bash
python -u /data/chapman/eclipse/FTatom/src/cns/phipsi_restraints.py \
-n alpha -t -110 -60 -50 30 \
-n beta -t -150 -60 70 -170 \
-n left_helix -t 40 60 20 50 -G \
namd_11_to_519.pdb namd_11_to_519_phipsi.cns