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News & Updates Official Release PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released on August 4, 2014. Official Release PyMOL, AxPyMOL, and JyMOL v1.7 have all been released today, January 14, 2014. 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. New Plugin GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS. New Software CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL. New Script cgo_arrow draws an arrow between two picked atoms. Tips & Tricks Instructions for generating movie PDFs using .mpg movies from PyMOL. 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.