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 > > > > Karl M. Oberholser, Ph.D. Phone: > Professor of Chemistry Voice: 717-766-0512 > Chemistry & Biochemistry Dept. Fax: 717-691-6046 > Messiah College e-mail: [EMAIL PROTECTED] > P.O. Box 3049 > One College Avenue > Grantham, Pa 17027 > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2005. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
