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News & Updates 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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