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 | PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation. Please support our mission to create open, effective, and affordable tools by purchasing a subscription to maintenance and/or support. Thanks! |
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Latest News |
December 1, 2008: The PyMOL Industrial Consortium has been announced and will launch at the start of 2009.
November 22, 2008: Nir London writes about PyMOL scripts in the Macromolecular Modeling Blog.
October 16, 2008: This week's PyMOL-based Nature cover pertains to crystal structures and models of the Sec ATPase and membrane protein-translocation channel (one article, two letters, one news & views).
September 24, 2008: More PyMOL-based Journal Covers: from the August 2008 issue of RNA Journal, an image inspired by Robertson and Scott, The structural basis of ribozyme-catalyzed RNA assembly. Science 315, 1549 (2007), and Cameron et al., Investigations on the evolutionary conservation of PCSK9 reveal a functionally important protrusion. FEBS 275, 4121 (2008).
September 23, 2008: PyMOL tips and links were posted to the Molecular Design Blog (hosted by the Rosetta Design Group).
September 20, 2008: We have updated this web site and are now making use of the issue trackers provided by SourceForge (see TRACKERS above) for the open-source project. Current PyMOL Support Subscribers are of course welcome to continue sending email requests directly to support@delsci.com.
September 18, 2008: Apple has fixed stereo 3D in Leopard! We can therefore happily recommend purchase of a Leopard-based Mac Pro for Stereo 3D visualization using MacPyMOL. However, if you also need other stereo 3D-capable software running under X11, then sit tight for now: a future version of Leopard's XQuartz should support this as well.
PyMOL Summary, Keywords, & Links: PyMOL is a molecular viewer developed in the spirit of RasMol and OpenRasMol and intended for visualization of 3D chemical structures including X-ray crystal structures of: proteins, nucleic acids (DNA, RNA, & tRNA), and carbohydrates, as well as small molecule structures of drug leads, inhibitors, metabolites, sugars, nucleoside phosphates, and other ligands including inorganic salts and solvent molecules. PyMOL serves academic research and education in chemistry and biology, and the biotechnology and pharmaceutical industries by rendering publication-quality journal illustrations of macromolecules including drug targets such as GPCRs, kinases (Abl, Raf, Aurora, EGFR), proteases (HIV, BACE, Factor Xa), phosophorylases (PTP1B), and other enzyme targets, as well as therapeutic biomolecules such as humanized antibodies, cytokines, hormones, and serpins. Available molecular representations include space-filling "CPK" atoms, chemical bonds, cartoon ribbons, molecular surfaces, and solvent accessible surface meshes. Molecular interactions can be represented using interatomic distances, van der Waals clashes, property-based, potential-based, & proximity-based coloring schemes, solid and mesh isosurface potentials, slice planes, and gradient field lines. PyMOL also supports input of electron density maps, electrostatic potential maps, and other volumetric data sets as well as arbitrary 3D geometries comprised of triangles, spheres, cylinders, cones, ellipsoids, and text. Output options include copy & paste, PNG images, QuickTime Movies (on Mac), VRML, Maya OBJ, and POV-Ray input files. Molecular animations can be created through simple object & camera motions or through input of trajectories from molecular dynamics simulations and other dynamic conformational ensembles such as 3D NMR structures, allosteric states, and Monte Carlo configurations. PyMOL can be scripted using Python and is available as both an ActiveX Control and a Java/JNI Component. PyMOL supports OpenGL stereo 3D display on devices such as Planar3D, ZScreen, and Christie MIRAGE. PyMOL integrates with the open source projects: APBS, mengine, and mpeg_encode via the FreeMOL open-source compilation, and can read PDB, PQR, MOL, SDF, MOL2, XPLOR, CCP4, DSN6, DX, TRJ, DCD, XTC, and GRID formatted files. PyMOL also integrates with the SEURAT data mining & collaboration tool from Synaptic Science and can read files written by Chemical Computing Group's "MOE" (Molecular Operating Environment), as well as Schrodinger's Maestro suite.
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Copyright © 2008 DeLano Scientific LLC. All rights reserved. |
The PyMOL open-source code is hosted at: |
