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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
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Revision as of 15:56, 5 December 2025

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Welcome to the PyMOL Wiki!
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Quick Links
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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...

Theseus

Included in psico
This command or function is available from psico, which is a PyMOL extension.

Module psico.fitting

theseus is a wrapper for the theseus program for maximum likelihood superpositioning of macromolecular structures. It produces results very similar to xfit.

Installation

For Linux and macOS, all dependencies are available from Anaconda Cloud: 

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c schrodinger theseus

Usage

Superpose two objects: 

theseus mobile, target [, match [, cov [, cycles [, mobile_state [, target_state [, exe [, preserve ]]]]]]]

Ensemble-fit states of a multi-state object: 

intra_theseus selection [, state [, cov [, cycles [, exe [, preserve ]]]]]

Arguments

  • mobile = string: atom selection for mobile atoms
  • target = string: atom selection for target atoms
  • match = string: in, like, align, none or the name of an alignment object (see local_rms help for details) {default: align}
  • cov = 0/1: 0 is variance ..→
A Random PyMOL-generated Cover. See Covers.


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