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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) GoogleSearch
Max OS X 10.8 Select_sites
News & Updates
X11 Libraries Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here X11 Libraries.
New Script select_sites can set author/paper selections according to SITE annotation in pdb file
New Script b2transparency can set surface transparency based on atom b-factor
New Extension psico is a python module which extends PyMOL with many commands
New Script uniprot_features makes named selections for sequence annotations from uniprot
New Plugin Gyration_tensor Calculates chain-wise gyration tensor of a protein.
New Script set_phipsi can set phi/psi angles for all residues in a selection
New Script dehydron A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack.
New Script pymol2glmol is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!
New Script cyspka is an experimental surface cysteine pKa predictor.
New Plugin Contact_Map_Visualizer visualize residues corresponding to the contact map
New Script spectrum_states colors states of multi-state object
New Script TMalign is a wrapper for the TMalign program
Gallery Updates The gallery has been updated to include a few new ideas and scripts for rendering
New Script save_settings can dump all changed settings to a file
Tips & Tricks Instructions for generating 3D PDFs using PyMOL.
Wiki Update Wiki has been updated. Please report any problems to the sysops.
New Scripts Create objects for each molecule or chain in selection with split_object and split_chains
New Script Rotkit: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function.
New Script Forster-distance-calculator: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See DisplacementMap.
New Script propka: Fetches the pka values for your protein from the propka server. propka generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.
Older News See Older News.
Did you know...

The DPL extension (version 2.3.0) produced a SQL statement which lead to a Database error.
The reason may be an internal error of DPL or an error which you made,
especially when using DPL options like titleregexp.
Query text is:
SELECT DISTINCT `pmw_page`.page_namespace AS page_namespace,`pmw_page`.page_title AS page_title,`pmw_page`.page_id AS page_id, `pmw_page`.page_title AS sortkey, `pmw_page`.page_counter AS page_counter FROM `pmw_page` INNER JOIN `pmw_categorylinks` AS cl0 ON `pmw_page`.page_id=cl0.cl_from AND (cl0.cl_to='Commands' OR cl0.cl_to='Plugins' OR cl0.cl_to='Script_Library' OR cl0.cl_to='Settings') WHERE 1=1 AND `pmw_page`.page_namespace IN ('0') AND `pmw_page`.page_is_redirect=0 ORDER BY page_title ASC LIMIT 500 OFFSET 0

Error message is:

A Random PyMOL-generated Cover. See Covers.