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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... Kabsch Note: PyMOL has built-in commands to do RMSD fitting. This script is typically not needed. In particular, optAlign (sele1), (sele2) is identical to fit (sele1), (sele2), matchmaker=-1. See also: fit, align. Type Python Script Download Author(s) Jason Vertrees License GPL Intro The Kabsch algorithm uses linear and vector algebra to find the optimal rotation and translation of two sets of points in N-dimensional space as to minimize the RMSD between them. The following program is a Python implementation of the Kabsch algorithm. This program when called will align the two selections, optimally, convert the proteins in the selection to ribbons and change the color of the selections to show the matched alignments. WHAT THIS DOESN'T DO: This program does NOT provide a pairwise alignment of two structures from scratch. You have to tell it what the equivalent ..→

A Random PyMOL-generated Cover. See Covers.