I thought that possibly the default was color structure, and I get those colors some times, but other times instead of getting gold for sheets I get white, blue and pink.
My concern several weeks ago was that when a button is pressed multiple times the axis are not displayed.  I have come to realize that each additional time the plot is made only the data points are put on the new frame.  The axis are not drawn on the additional frames.

>>> Bob Hanson <> 9/26/2007 2:39 PM >>>
Karl Oberholser wrote:

> What, if anything, determines the color of the spheres in the
> Ramachandran plot or is it completely random?

I think the default is "color structure" so pink is helix, gold is
sheet, and blue is turn, and white is other. The dots are just atoms,
and they correspond specifically to the C-alpha carbons of the peptides.

Karl, I think you mentioned something a while back about axes. I haven't
looked into that, but if you want to work with me on this, I could
start. Really the Ramachandran plots are very new -- a direct outgrowth
of this summer's Gordon Research Conference on Visualization that I
attended. You are probably the first to try anything with them, and I
would expect there could be all sorts of modifications that need to be
done regarding them. I do feel that they are just "sketched out " in the
code. Lots of room for improvement.

One thing I introduced with the Ramachandran plots was the concept of a
"dataframe" -- a frame that doesn't rotate with the other models but
instead has its own independent rotational character. It was tested
some, but not fully. I know I need to think about that some more.


> Karl

> Karl M. Oberholser, Ph.D.         Phone:
> Professor of Chemistry                 Voice: 717-766-0512
> Chemistry & Biochemistry Dept.   Fax: 717-691-6046
> Messiah College                        e-mail:
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Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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