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Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
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Gallery | Covers PyMOL Cheat Sheet (PDF) GoogleSearch
News & Updates
Official Release PyMOL, AxPyMOL, and JyMO v1.7 have all been released] today, January 14, 2014.
New Plugin Bondpack is a 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.
New Plugin GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS.
New Software CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
New Script cgo_arrow draws an arrow between two picked atoms.
Tips & Tricks Instructions for generating movie PDFs using .mpg movies from PyMOL.
Older News See Older News.
Did you know...

Find buried waters

This script finds and turns a selection of waters determined to be buried (no solvent accessibility) in the original selection. If you prefer to define your own cutoff of "accessible" use the 2nd parameter.

Usage

find_buried_waters [ sele [, cutoff [, state ]]]

Script

<source lang="python"> from pymol import cmd

def find_buried_waters(sele='all', cutoff=-1, state=1, quiet=1, _self=cmd):

   

DESCRIPTION

   Finds and turns a selection of waters determined to be buried (no solvent
   accessibility) in the original selection.

ARGUMENTS

   sele = string: atom selection {default: all}
   cutoff = float: threshold on what one considers an "exposed"
   atom (in A**2) {default: surface_residue_cutoff}
   state = int: object state {default: 1}
   
   cutoff, state, quiet = float(cutoff), int(state), int(quiet)
   tmpObj=_self.get_unused_name("__tmp")
   _self.create(tmpObj, sele, state, 1, zoom=0)
   _self.set("dot_solvent", 1, tmpObj);
   _self.get_area(tmpObj, state=1, load_b=1)
   if cutoff <  ..→
A Random PyMOL-generated Cover. See Covers.