Main Page

hosted by

Welcome to the PyMOL Wiki!

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

To request a new account, email SBGrid at: 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 POSF New PyMOL fellows announced for 2018-2019 Tutorial Plugins Tutorial updated for PyQt5 Official Release PyMOL v2.2 has been released on July 24, 2018. New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures. Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll! Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons Older News See Older News.

Did you know... Orient orient aligns the principal components of the atoms in the selection with the XYZ axes. The function is similar to the orient command in X-PLOR. USAGE orient object-or-selection [, state] orient (selection) PYMOL API cmd.orient( string object-or-selection [, state = 0] ) NOTES state = 0 (default) use all coordinate states state = -1 use only coordinates for the current state state > 0 use coordinates for a specific state EXAMPLES For models with NCS symmetry, orient will align the model with the symmetry axis centered along the viewport's z axis. For example, fetch 1hiw, async=0 as cartoon remove (!chain A,B,C) orient util.cbc will produce the first image below. However, if there is a larger symmetry, e.g. two trimers, this will not work. In the above example, leaving out remove (!chain A,B,C) from the script results in the second image below. <gallery> Image:1hiw orient.png|One trimer from 1hiw after "orient" ..→

A Random PyMOL-generated Cover. See Covers.