Dssp

From PyMOLWiki
Jump to: navigation, search

Included in psico
This command or function is available from psico, which is a PyMOL extension.

Module psico.editing

dssp is a wrapper for the popular DSSP program, which computes secondary structure. The command updates PyMOL's ss atom property.

Installation

The dssp command is available from the psico package and requires the dssp binary (or mkdssp, dsspcmbi, dssp-2).

All dependencies are available from Anaconda Cloud:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c salilab -c speleo3 dssp 

Usage

dssp [ selection [, exe [, raw [, state ]]]]

Arguments

  • selection = str: atom selection {default: all}
  • exe = str: path to dssp binary {default: search $PATH for dsspcmbi, dssp, dssp-2, mkdssp}
  • raw = str: atom property to assign the dssp secondary structure type to. This type will also be translated to PyMOL's H/S/L types and assiged to the ss property {default: }
  • state = int: object state {default: -1 (current state)}

Example

import psico.editing
fetch 1ubq, async=0

dssp all, raw=custom

color gray
color red, custom H
color orange, custom G
color yellow, custom E
color wheat, custom B
color forest, custom T
color green, custom S
set cartoon_discrete_colors, 1

See Also