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News & Updates Official Release PyMOL v1.8.2 has been released on April 20, 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... Translate And Measure To use, you would call it like : print translateAndMeasure("molA", "molB", [1,0,0], 4) which would print "overlap" if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X. Of course, this could be improved to report exactly which atoms were overlapping, or to make distance objects (using cmd.distance) to show them. <source lang="python"> def translateAndMeasure(selection, other, translationVector, cutoff): cmd.translate(translationVector, selection) return checkDistances(selection, other, cutoff) def checkDistances(moleculeA, moleculeB, cutoff): ids_A = getIds(moleculeA) ids_B = getIds(moleculeB) for idA in ids_A: for idB in idsB: d = distance(moleculeA, idA, moleculeB, idB) if d > cutoff: return "overlap" return "no overlap" def distance(a, idA, b, idB): atomA = "%s and id %s" % (a, idA) atomB = "%s and id %s" % (b, idB) return cmd.get_distance(atomA, atomB) def getIds(selection): ..→

A Random PyMOL-generated Cover. See Covers.