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Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
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Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
Official Release PyMOL v2.2 has been released on July 24, 2018.
POSF PyMOL Open-Source Fellowship program accepting applications for 2018-2019
New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
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...


set is one of the most utilized commands. PyMOL representations, states, options, etc. are changed with set. Briefly, set changes one of the PyMOL state variables. Currently there are over 600 PyMOL settings!


# set '''name''' to '''value'''
set name, [,value [,object-or-selection [,state ]]]

# alternative way to do the above.
set name = value  # (DEPRECATED)


cmd.set ( string name, 
    string value=1,
    string selection='',
    int state=0,
    int updates=1,


set surface_color, red

set ray_trace_mode, 3

set ribbon_width, 4

# set the label size to 2Ang.
set label_size, -2


The default behavior (with a blank selection) changes the global settings database. If the selection is 'all', then the settings database in all individual objects will be changed. Likewise, for a given object, if state is zero, then the object database will be ..→

A Random PyMOL-generated Cover. See Covers.