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

bosco apposite at gmail.com
Thu Sep 14 02:19:51 EDT 2006

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.


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

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

blog: inthestates.blogspot.com
site: bosco.infogami.com

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