[Molvis-list] Software Release: Ramachandran Plot Explorer version 1.0

Jeff Cohlberg cohlberg at csulb.edu
Thu Sep 14 14:39:39 EDT 2006


I successfully downloaded and launched the Mac version of the program, 
but I don't know how to use it.  When I click on the Help menu with my 
mouse, nothing happens.  Is there a set of instructions for using the 
program available?


bosco wrote:

> I've been hard at work coding up the next release of my program. I'm
> releasing it as 1.0 because I think it's finally got a reasonable set
> of features. There are versions for MacOsx, Linux GTK, and Windows.
> http://bosco.infogami.com/rama
> The design of the program is to allow you to easily see the
> Ramachandran plot (phi-psi angles) and the chi angles of a protein
> structure. You can explore conformation changes (phi/psi/chi angles)
> easily with a mouse.
> In order to see how conformation changes affect the protein, Ive included
> real-time calculation of H-bonds, weak H-bonds and (now) steric
> clashes. This makes it easy to see why regions of the Ramachandran
> plot are forbidden, and why some sidechain chi angles are favoured.
> I've included, what I think, is a necessary set of navigating tools
> (sequence bar, z-slab-bar, and lots of visual cues).
> It's also the only program I know that deals properly with proline ring
> conformations.
> There is a 3-point-clamp function, that (1) explores discrete
> solutions of a loop with fixed anchors and 3 hinge-residues, and (2)
> allows the exploration of the phi/psi angles of residues *inside* the
> clamp. The clamp prevents these phi/psi changes from disturbin the
> rest of the protein.
> You should be able to easily edit (cut/paste/insert) the sequence of
> the protein, and explore mutation, with a mouse.
> I've bent over backward to make sure new version uses native widgets
> (file open/save dialogs are standard!) and you can resize the window
> to your heart's content.
> So enjoy the program, and of course, email me for bug-reports,
> suggestions, anything.
> Bosco Ho
> Agard Lab, UCSF

Jeffrey A. Cohlberg, Professor
Department of Chemistry and Biochemistry
California State University, Long Beach
Long Beach, CA 90840
562-985-4944		fax 775-248-1263
cohlberg at csulb.edu

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