Main Page

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 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 v1.7.2 have all been released on August 4, 2014. Official Release PyMOL, AxPyMOL, and JyMOL 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... Color by conservation Type Python Script Download scripts/color_by_conservation.py Author(s) Jason Vertrees License Free This code has been put under version control in the project Pymol-script-repo Overview This script reads an alignment object and colors the protein objects in the alignment by the sequence conservation found in the alignment. Example Usage reinitialize import color_by_conservation # get some kinases fetch 1opk 3dtc 3p86 2eva 3efw, async=0 # turn on the sequence viewer set seq_view # align them into the "algn" object for x in cmd.get_names(): cmd.align(x, "3efw and c. A", object="algn") # color color_by_conservation aln=algn, as_putty=1

A Random PyMOL-generated Cover. See Covers.