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

[bosco]

Hi Jeff,

I haven't written a tutorial for it yet but it should be pretty easy to
discover features. The help menu is a default item in the gui library.

Anyway to get you started:

1. click on a residue on the protein - this should select the residue and
the residue will turn green. It's phi/psi angle should then appear in the
Ramachandran plot in the bottom left hand corner.

2. drag the green dot in the Ramachandran plot

3. click on the word measure on the bottom right hand corner

4. now click on any 2 atoms to measure the distance between the atoms

Bosco



On 9/14/06, Jeff Cohlberg <cohlberg at csulb.edu> wrote:
>
> Bosco--
>
> 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?
>
> Jeff
>
>
>
>
> 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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-- 
blog: inthestates.blogspot.com
site: bosco.infogami.com