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Revision as of 06:32, 11 January 2016

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
New accounts: email jason (dot) vertrees (@) gmail dot com
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
Official Release PyMOL v1.8.0 has been released on Nov 18, 2015.
PyMOL Open-Source Fellowship Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released on May 4, 2015.
New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
New Plugin Bondpack is a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce PyMOL can now be visualized in 3D using Nvidia GeForce video cards (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
Older News See Older News.
Did you know...

Grepsel

Create selections matching motifs, using python regular expression syntax.

This is very similar to the FindSeq script.

The Code

<source lang="python">

  1. Create named selections using regular expressions for the protein sequence

import pymol import re cmd = pymol.cmd

aa = { 'ASP' : 'D' , 'GLU' : 'E' , 'GLN' : 'Q' , 'ASN' : 'N' , 'SER' : 'S' , 

      'THR' : 'T' , 'CYS' : 'C' , 'HIS' : 'H' , 'ARG' : 'R' , 'LYS' : 'K' ,
      'MET' : 'M' , 'ALA' : 'A' , 'ILE' : 'I' , 'LEU' : 'L' , 'VAL' : 'V' ,
      'GLY' : 'G' , 'PRO' : 'P' , 'TRP' : 'W' , 'PHE' : 'F' , 'TYR' : 'Y' ,
      'SCY' : 'U' , 'ASX' : 'B' , 'GLX' : 'Z' , 'XXX' : 'X'}
  1. made this before the sequence view option, probably another way to do it now

def seqoneint(model): 

  pymol.stored.seq = []
  cmd.iterate("%s and name ca"%model,"stored.seq.append(resn)")
  seq = ""
  for x in pymol.stored.seq:
     if aa.has_key(x):
        res = aa[x]
        seq = seq+res
     else:
        seq = seq + '-'
  return seq


def grepsel(selection="(all)",stretch="",pre ..→

A Random PyMOL-generated Cover. See Covers.


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