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News & Updates Poll New protein/nucleic selection keywords for PyMOL - Tell us what you think! Official Release PyMOL v2.0 has been released on September 20, 2017. 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... Ss A command to list a summary of the secondary structure for a selection. Use like "ss my_protein" where "my_protein" is the name of the chain or structure in view. from pymol import cmd from pymol import stored def ss(selection): class SSE(object): def __init__(self, start, typ): self.start, self.typ = start, typ self.end = -1 def __repr__(self): return "%s-%s %s" % (self.start, self.end, self.typ) stored.pairs = [] cmd.iterate("%s and n. ca" % selection, "stored.pairs.append((resi, ss))") num, currentType = stored.pairs[0] sses = [SSE(num, currentType)] currentSSE = sses[0] for resi, ssType in stored.pairs: if ssType == currentType: currentSSE.end = resi else: sses.append(SSE(resi, ssType)) currentSSE = sses[-1] currentType = ssType for sse in sses: print sse cmd.extend("ss", ss) ..→

A Random PyMOL-generated Cover. See Covers.