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News & Updates Official Release PyMOL, AxPyMOL, and JyMO v1.7 have all been released today, January 14, 2014. 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. New Plugin GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS. New Software CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL. New Script cgo_arrow draws an arrow between two picked atoms. Tips & Tricks Instructions for generating movie PDFs using .mpg movies from PyMOL. Older News See Older News.

Did you know... Intra fit intra_fit fits all states of an object to an atom selection in the specified state. It returns the rms values to python as an array. USAGE intra_fit (selection),state PYMOL API cmd.intra_fit( string selection, int state ) EXAMPLES Simple Selection intra_fit ( name ca ) Fitting NMR Ensembles Warren provided a great example on the PyMOL list. If the NMR ensemble has all the structures loaded as multiple states (which is the default behavoir (see split_states) for multimodel PDBs) then we can simply call: print cmd.intra_fit(selection, state) which will fit all of the other states to the indicated states and return the RMS values as a list. A simple example is: <source lang="python"> fetch 1i8e, async=0 print cmd.intra_fit("1i8e////CA", 1) ..→

A Random PyMOL-generated Cover. See Covers.