AMBER Archive (2005)

Subject: AMBER: recent Chimera MD enhancements

From: Eric Pettersen (pett_at_cgl.ucsf.edu)
Date: Tue Nov 15 2005 - 14:59:16 CST

Hi,
        I thought people here on the list might be interested in some recent
improvements in Chimera's MD capabilities. The most recent release
offers a simplified interface for recording trajectory movies, the
ability to compute and display the occupancy of certain atoms
relative to others (e.g. solvent in a binding site), and much faster
computation of the all-by-all RMSD map than in previous releases.
Also, some people may not be aware of the previously-available "hold
steady" feature wherein any part of a structure can be held as steady
as possible as a trajectory is played -- which can be particularly
useful when viewing a replica-exchange trajectory.
        You can find full documentation for the MD features here: http://
www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html
        There is a tutorial here: http://www.cgl.ucsf.edu/chimera/docs/
UsersGuide/tutorials/ensembles2.html

        The main page for Chimera is here: http://www.cgl.ucsf.edu/chimera

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett_at_cgl.ucsf.edu
                         http://www.cgl.ucsf.edu

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