Main Page

Welcome to the PyMOL Wiki!

The community-run support site for the PyMOL molecular viewer.

To request a new account, email 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 v1.8.2 has been released on April 20, 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... Color By Mutations This script creates an alignment of two proteins and superimposes them. Aligned residues that are different in the two (i.e. mutations) are highlighted and colored according to their difference in the BLOSUM90 matrix. It is meant to be used for similar proteins, e.g. close homologs or point mutants, to visualize their differences. Example color_by_mutation protein1, protein2 Example: rat trypsin and cow trypsin colored by color_by_mutation. <source lang="python"> created by Christoph Malisi. Creates an alignment of two proteins and superimposes them. Aligned residues that are different in the two (i.e. mutations) are highlighted and colored according to their difference in the BLOSUM90 matrix. Is meant to be used for similar proteins, e.g. close homologs or point mutants, to visualize their differences. from pymol import cmd aa_3l = ..→

A Random PyMOL-generated Cover. See Covers.