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 Official Release PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released on December 3, 2014. New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL. 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... Translate And Measure To use, you would call it like : print translateAndMeasure("molA", "molB", [1,0,0], 4) which would print "overlap" if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X. Of course, this could be improved to report exactly which atoms were overlapping, or to make distance objects (using cmd.distance) to show them. <source lang="python"> def translateAndMeasure(selection, other, translationVector, cutoff): cmd.translate(translationVector, selection) return checkDistances(selection, other, cutoff) def checkDistances(moleculeA, moleculeB, cutoff): ids_A = getIds(moleculeA) ids_B = getIds(moleculeB) for idA in ids_A: for idB in idsB: d = distance(moleculeA, idA, moleculeB, idB) if d > cutoff: return "overlap" return "no overlap" def distance(a, idA, b, idB): atomA = "%s and id %s" % (a, idA) atomB = "%s and id %s" % (b, idB) return cmd.get_distance(atomA, atomB) def getIds(selection): ..→

A Random PyMOL-generated Cover. See Covers.