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News & Updates PyMOL Open-Source Fellowship Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship 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... ColorByRMSD Type Python Module Download scripts/colorbyrmsd.py Author(s) Shivender Shandilya, Jason Vertrees, Thomas Holder License BSD-2-Clause This code has been put under version control in the project Pymol-script-repo Introduction This script allows you to color two structures by Root Mean Square Deviation (RMSD). The distances between aligned C-alpha atom pairs are stored as B-factors of these residues, which are colored by a color spectrum, with blue specifying the minimum pairwise RMSD and red indicating the maximum. Unaligned residues are colored gray. Usage colorbyrmsd mobile, target [, doAlign [, doPretty [, guide [, method ]]]] Arguments mobile = string: atom selection for mobile atoms target = string: atom selection for target atoms doAlign = 0 or 1: Superpose selections before calculating distances {default: 1} doPretty = 0 or 1: Show nice representation and colors {default: 1} guide = 0 or 1: Only use C-alpha atoms {default: 1} method = align ..→

A Random PyMOL-generated Cover. See Covers.