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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... 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.