Main Page

From PyMOLWiki
Jump to: navigation, search
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
News & Updates
Official Release PyMOL, AxPyMOL, and JyMO v1.7 have all been released today, January 14, 2014.
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.
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...


Issuing the Python command will put you into a stateful pseudo-interactive Python session. Or, more simply it's stateful in that you can invoke the Python session write some code, end the session, then restart the session and your data will be saved (see Example 1). It's pseudo-interactive in that you don't get feedback until you type "python end," upon which your code is run the output appears.

This is a helpful command for testing different scripting or state-editing strategies for movie making.


# start the session
# ...
# your Python code goes here
# ...
# end the session
python end


  • Start the session. Set x to 10. End the session. Restart the session and see if the value of x is recalled.
x = 10
print x
python end
print x
python end



Python Version

Python scripts and commands used within PyMOL can only be written using the current version of ..→

A Random PyMOL-generated Cover. See Covers.

Personal tools