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News & Updates Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL Official Release PyMOL v1.8.6 has been released on March 9, 2017. Official Release PyMOL v1.8.4 has been released on October 4, 2016. 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. Official Release PyMOL v1.8.0 has been released on Nov 18, 2015. 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 v1.7.6 have all been released on May 4, 2015. 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.

Did you know... Count molecules in selection = Overview = This script will return the number of distinct molecular objects in a given selection. If no selection is given, the script assumes "sele" the named mouse selection. Example # run the script run count_molecules_in_sel.py # grab a protein from the PDB fetch 2f56, async=0 # select all the urea molecules select resn URE # should count 11 molecules count_molecules_in_selection # change the selection and try again select polymer # should return 3, as there's 3 chains count_molecules_in_selection The Code <source lang="python"> import pymol from pymol import cmd def count_mols_in_sel(sel="sele"): """ Returns the number of distinct molecules in a given selection. """ sel_copy = "__selcopy" cmd.select(sel_copy, sel) num_objs = 0 atoms_in_sel = cmd.count_atoms(sel_copy) while atoms_in_sel > 0: num_objs += 1 cmd.select(sel_copy, "%s and not (bm. first %s)" % (sel_copy, sel_copy)) atoms_in_sel = cmd.count_atoms(sel ..→

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