Pymol supports two modes of input: point and click mode, and command line mode. Stereo mode is a convenient way to see 3D. Stereo: the stereo option controls whether or not PyMOL displays the scene in stereomode. Then carrys out zero or more cycles of refinement in order to reject structural outliersfound during the fit. align: align performs a sequence alignment followed by a structural alignment, and Symmetry: generate symmetry objects of your molecule. Nolly surface or the surface that would be traced out by the surfaces of waters incontact with the protein at all possible positions. The simplest actions are:Ĭlose-up: zoom-in and out surface/map: The surface representation of a protein, in PyMol, shows the Con. phi Delphi/Grasp Electrostatic Potential MapOnce your structure is loaded, you can modify it. cc2 ChemDraw 3D cartesian coordinate file ccp4 CCP4 map file (BINARY) to be loaded on startup xplor X-PLOR Map file (ASCII) to be loaded on startup sdf MDL SD file to be parsed and loaded on startup mol MDL MOL file to be loaded on startup mmod Macromodel format to be loaded on startup
pdb Protein Data Bank format file to be loaded on startup pml PyMOL command script to be run on startup To visualize a 3D structure the file has to be in the right format. PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation. PyMOL is a molecular viewer, render tool, and 3D molecular editor intended for visu-alization of 3D chemical structures including atomic resolution X-ray crystal structuresof: proteins, nucleic acids (DNA, RNA, and tRNA), and carbohydrates, as well as smallmolecule structures of drug leads, inhibitors, metabolites, sugars, nucleoside phosphates,and other ligands including inorganic salts and solvent molecules.
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