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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
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! Poll
 
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| [https://goo.gl/forms/r0Ck03VTytZQxN4A2 New protein/nucleic selection keywords for PyMOL] - Tell us what you think!
 
 
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! Official Release
 
! Official Release
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| [https://pymol.org PyMOL v2.0 has been released] on September 20, 2017.
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
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! Plugin Update
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! Python 3
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
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! Official Release
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! POSF
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| [http://pymol.org PyMOL v1.8.6 has been released] on March 9, 2017.
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 
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! Official Release
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! Tutorial
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| [http://pymol.org PyMOL v1.8.4 has been released] on October 4, 2016.
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| [[Plugins Tutorial]] updated for PyQt5
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! New Script
 
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
 
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! New Plugin
 
! New Plugin
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| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
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| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 
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! Official Release
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! Selection keywords
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| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
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| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
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! PyMOL Open-Source Fellowship
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! Plugin Update
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| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 
|-
 
|-
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! Official Release
+
! New Script
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| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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|-
 
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! New Plugin
 
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| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
 
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! New Plugin
 
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| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
 
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|-
 
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! New Plugin
 
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| [[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.
 
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! 3D using Geforce
 
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| 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.
 
 
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! Older News
 
! Older News

Latest revision as of 03:21, 22 June 2021

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Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
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 fellows announced for 2018-2019
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 items ..→

A Random PyMOL-generated Cover. See Covers.


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