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Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
Official Release PyMOL v1.8.4 has been released on October 4, 2016.
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.
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...

Launching From a Script

The recommended way to run PyMOL-Python scripts is by using PyMOL as the interpreter. This is supported by all versions of PyMOL, including the pre-compiled bundles provided by Schrödinger.

Example from a shell:

shell> pymol -cq script.py

With arguments (sys.argv becomes ["script.py", "foo", "bar"]):

shell> pymol -cq script.py -- foo bar

Example from a running PyMOL instance:

PyMOL> run script.py

For advanced users, the following PyMOL versions also allow to run PyMOL from an existing Python process:

  • PyMOL 2.0 based on Anaconda (using Anaconda's python, which is included in bundles provided by Schrödinger)
  • Open-Source PyMOL
  • Schrödinger-provided "Mac alternative X11-only build" of the 1.8.x series

After importing the pymol module, PyMOL's event loop has to be started with a call to pymol.finish_launching() (not supported on macOS).

Usage

With PyMOL 2.1, calling any ..→

A Random PyMOL-generated Cover. See Covers.