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The community-run support site for the PyMOL molecular viewer.
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News & Updates
New Setup	PyMOL-open-source-windows-setup v3.1 has been released on January 20, 2025. More information under Windows Install.
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...
MakeVinaCommand = Overview = Vina is a new, very fast, molecular docking program, written by Oleg Trott. In order to run Vina, you should have MGLTools1.5.4 installed (you need prepare_receptor4.py and prepare_ligand4.py). But, you don't need MGLTools for this script to run. To run Vina it needs to know the center of the protein and also its extents (size in XYZ directions). We can easily do this with PyMOL. Requirements: COM -- simple script to get the center of mass of a selection Todo: Commandline options Robustness to vagaries of input Usage & Help Usage pymol -cq ./makeVinaCommandFromProtein.py proteinFile ligandFile For high-throughput screening, where we compare each ligand to each protein, I typically wrap the script in a for-loop like: <source lang="bash"> foreach protein in my proteins directory for protein in proteinsDir/; do # foreach ligand in my ligands directory for ligand in ligandsDir/; do; # make a ..→

Usage