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

bosco apposite at gmail.com
Fri Sep 15 02:06:11 EDT 2006

I've been hard-at-work coding up this release of my protein viewer.
It's 1.0 because I think it's finally got a reasonable set of

Download the program (open-source) at http://bosco.infogami.com/rama
with versions for MacOsx, Linux GTK, and Windows.

The Ramachandran Plot Explorer is designed to make it easy to examine
the conformation of a polypeptide - through the interactive
Ramachandran plot (phi-psi angles) and chi angle box, simply by
dragging the mouse.

To see how these conformational changes affect the energetics, I've
included real-time calculation of H-bonds, weak H-bonds and (now)
steric clashes. This makes it easy to see why certain regions of the
Ramachandran plot are forbidden, and why certain 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 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 disturbing the
rest of the protein.

You should be able to easily edit (cut/paste/insert) the sequence of
the protein, and mutate residues.

This 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 email me for bug-reports, suggestions, anything.

Bosco Ho
Agard Lab, UCSF

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

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