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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
|-
! POSF
! New Setup
| [https://pymol.org/fellowship PyMOL Open-Source Fellowship program] accepting applications for 2018-2019
| [https://github.com/kullik01/pymol-open-source-windows-setup/releases/tag/v3.1.0 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 [https://github.com/sokrypton/ColabFold ColabFold] to enable the prediction and analysis of 3D protein structures for the scientific end-user. [https://github.com/urban233/PySSA/releases/tag/v1.0.1 v1.0 has been released] on July 10, 2024.
|-
! Official Release
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
|-
! New Plugin
! New Plugin
| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
| [[CavitOmiX|CavitOmiX]] calculate [https://innophore.com Catalophore™ cavities], predict protein structures with [https://www.nvidia.com/en-us/gpu-cloud/bionemo OpenFold by NVIDIA-BioNeMo], [https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/ ESMFold] and retrieve [https://www.deepmind.com/research/highlighted-research/alphafold Alphafold] models
|-
|-
! Official Release
! Official Release
| [https://pymol.org PyMOL v2.1 has been released] on March 13, 2018.
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
! New Plugin
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
|-
! Selection keywords
! Selection keywords
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! New Script
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
! New Plugin
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
|-
! New Plugin
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
|-
! New Plugin
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
|-
! New Plugin
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
|-
! 3D using Geforce
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
|-
|-
! Older News
! Older News

Latest revision as of 15:56, 5 December 2025

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Welcome to the PyMOL Wiki!
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To request a new account, email SBGrid at: accounts (@) sbgrid dot org
Quick Links
Tutorials Table of Contents Commands
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Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
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.


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