PyMOL

PyMOL Summary, Keywords, & Links: PyMOL is a molecular viewer, render tool, and 3D molecular editor developed in the spirit of RasMol and OpenRasMol and intended for visualization of 3D chemical structures including atomic resolution 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 for nanotechnology pictures include space-filling "CPK" atoms, chemical bonds, cartoon ribbons, molecular surfaces, and solvent accessible surface meshes. As a stereochemistry viewer, PyMOL can illustrate the 3D stereochemical relationships of organic chemistry. As a crystallographic protein structure viewer, PyMOL can display millions of atoms inside a crystal lattice. 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 POVRay POV 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 hardware from nVidia (3D Vision), ATI/AMD, and Intel, with stereoscopic 3D graphics display on devices such as the Planar3D, Samsung SyncMaster 2233RZ, Viewsonic Fuhzion VX2265wm & PJD6220-3D, ZScreen, and Christie MIRAGE with stereo 3D glasses or goggles. PyMOL integrates with the open source projects: APBS, mengine, and mpeg_encode via the FreeMOL open-source compilation, and can read PDB (protein data bank), 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 molecular modelling files written by Chemical Computing Group's "MOE" (Molecular Operating Environment), as well as Schrödinger's Maestro suite.

http://www.pymol.org