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... AAindex Type Python Script Download aaindex.py Author(s) Thomas Holder License BSD This code has been put under version control in the project Pymol-script-repo Included in psico This command or function is available from psico, which is a PyMOL extension. Module psico.aaindex Introduction Hydrophobicity coloring with KYTJ820101 AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. See http://www.genome.jp/aaindex/ This script is a python parser for the AAindex flat files which will be downloaded from ftp://ftp.genome.jp/pub/db/community/aaindex/ The script provides two PyMOL commands (but can also be used without PyMOL). aaindex2b: Loads numerical indices from aaindex1 as b-factors into your structure pmf: Potential of Mean Force (aaindex3) Python Example Consider the script is called aaindex.py, it is placed somewhere in your PYTHONPATH and the aaindex flatfiles are found in the current directory. <source lang="python"> import aaindex aaindex.init(path='.') aaindex.grep ..→

A Random PyMOL-generated Cover. See Covers.