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 New Plugin PySSA aims to combine PyMOL and ColabFold to enable the prediction and analysis of 3D protein structures for the scientific end-user. v1.0 has been released on July 10, 2024. Official Release PyMOL v3.0 has been released on March 12, 2024. New Plugin CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models Official Release PyMOL v2.5 has been released on May 10, 2021. Python 3 New Python 3 compatibility guide for scripts and plugins POSF New PyMOL fellowship announced for 2022-2023 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... Show contacts Introduction PyMOL Plugin for displaying polar contacts. Good hydrogen bonds (as determined by PyMOL) are shown in yellow. Electrostatic clashes (donor-donor or acceptor-acceptor) are shown in red. Close (<4.0 A) but not ideal contacts are shown in purple. Cutoffs are configurable. Exports the command `contacts` which takes two selections and an optional name for the generated contacts group. Alternatively, the selections can be chosen using a dialog box accessible from the Plugins menu. Usage show_contacts sel1, sel2, result="contacts", cutoff=3.6, bigcutoff=4.0 Required Arguments sel1 = first selection sel2 = second selection Optional Arguments result = name of created group containing contacts cutoff = cutoff for good contacts (yellow dashes) bigcutoff = ..→

A Random PyMOL-generated Cover. See Covers.