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News & Updates Official Release PyMOL, AxPyMOL, and JyMO 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... Cluster mols cluster_mols is a PyMOL plugin that allows the user to quickly select compounds from a virtual screen to be purchased or synthesized. It helps the user by automatically clustering input compounds based on their molecular fingerprints [1] and loading them into the PyMOL window. cluster_mols also highlights both good and bad polar interactions between the ligands and a user specified receptor. Additionally there are a number of keyboard controls for selecting and extracting compounds, as well as functionality for searching online to see if there are vendors for a selected compound. Description The basic work flow of cluster_mols.py can be broken up into three parts. Computing a similarity matrix from the input compounds Performing hierarchical clustering on the results from 1) Cutting the tree at a user-specified height and creating and sorting clusters The results of 1 and 2 are saved to python pickle files so you do not have to recompute them ..→

A Random PyMOL-generated Cover. See Covers.