Re: [Jmol-users] Ramachandran plot

[Bob H. <ha...@st...>]

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.

Bob

>  
> Karl
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>  
>  
> Karl M. Oberholser, Ph.D.         Phone:
> Professor of Chemistry                 Voice: 717-766-0512
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> Messiah College                        e-mail: obe...@me...
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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