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... Sphere scale ==Overview== This setting affects the apparent radius of spheres in the sphere representation. Default scale is set to 1.0. Syntax # set the sphere scale to size for selection. cmd.set ("sphere_scale", size=1, selection='', state=0, updates=1, log=0, quiet=1) # generally it's simpler to use the console form set sphere_scale, size, selection # you can print the current value for sphere_scale get sphere_scale size can be any floating point number, selection is the name of a selection. Examples Using 0.25 gives a nice balls&sticks representation with both lines and spheres turned on. set_bond stick_color, white, (all), (all) set_bond stick_radius, 0.14, (all), (all) set sphere_scale, 0.25, (all) show sticks show spheres set sphere_scale by itself will revert to default. Here you'll get a simple VDW rapresentation. <source lang="python"> set_bond stick_color, blue, (all), (all) set_bond stick_radius, 0.3, (all), (all) set sphere_transparency, ..→

A Random PyMOL-generated Cover. See Covers.