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Revision as of 05:12, 8 May 2018 by MarkoJukic (talk | contribs) (added new plugin news)
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News & Updates
New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
Official Release PyMOL v2.1 has been released on March 13, 2018.
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
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
New Plugin 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 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce PyMOL can now be 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 See Older News.
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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.


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


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 ]]]]]


  • 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.