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! Python 3
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
! Official Release
| [https://pymol.org PyMOL v2.3 has been released] on February 11, 2019.

Latest revision as of 05:05, 5 March 2021

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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
Official Release PyMOL v2.4 has been released on May 20, 2020.
Python 3 New Python 3 compatibility guide for scripts and plugins
POSF New PyMOL fellows announced for 2018-2019
Tutorial Plugins Tutorial updated for PyQt5
New Plugin PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
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...


protect protects a set of atoms from tranformations performed using the editing features. This is most useful when you are modifying an internal portion of a chain or cycle and do not wish to affect the rest of the molecule.


protect (selection)


cmd.protect(string selection)


This example makes a very cool little, and fake, molecular movie. Copy/paste this into PyMOL: <source lang="python"> load $PYMOL_PATH/test/dat/pept.pdb, obj

  1. create the fake trajectory (of states)

for a in range(2,31): cmd.create("obj","obj",1,a)

  1. remove the bond

unbond 5/C, 6/N

  1. This protects everything but all atoms witing 4
  2. Ang. of residue 5's carbon and residue 6's nitrogen.

protect not ((5/C or 6/N) extend 4)

  1. do some quick sculpting

sculpt_activate obj, 30 sculpt_iterate obj, 30, 100 smooth obj, 30, 3

  1. then program a bond-break/re-form movie

mset 1 x30 1 -30 30 x30 30 -1 mdo 45: unbond 5/C, 6/N, quiet=1 mdo 100: bond 5/C, 6/N, quiet=1

frame 100

as sticks orient ..→

A Random PyMOL-generated Cover. See Covers.