Bob, I have come to realize that you can control the color of the Ramachandran plot by placing the color command after the ramachandran command.
I want to do two or more plots, set their color to unique values and then overlay their display. I have tried using the following script after making plots in frames 2.1 & 4.1, but nothing is displayed. Does the frame all; display (*/n, */p) commands work with decimal values? The last three lines (between the #'s) are not part of the script that I run. frame 2.1 select all color red # Even when unique colors are set at the time of plot construction, they revert to color structure and have to be re-set. If I run 'frame 2.1; display all' after the plot is constructed, I have to insert the color command to control the color of the plotted spheres. frame 4.1 select all color gold frame all display ( */2 or */4 ) # 2073 atoms hidden select all color structure # Karl > >>>> Bob Hanson <[EMAIL PROTECTED]> 9/27/2007 5:12 PM >>> >let's talk about what you expect to see and what actually happens. For >example, I can see how if there were a ramachandran button on the page, >that would get pressed over and over. Now, it is possible that sometimes >one would have multiple plots. Perhaps there should be some automatic >way that for a given selection there is only ONE ramachandran frame. I >don't know.... > >Karl Oberholser wrote: > >> Bob, >> 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. >> >> Karl >> >> >> >>> Bob Hanson <[EMAIL PROTECTED]> 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. >> >> 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 & nbsp; >> > 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 >> <https://lists.sourceforge.net/lists/listin%0A%20%0A%20fo/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 >> <https://lists.sourceforge.net/lists/listinfo/jmol>-users >> >>------------------------------------------------------------------------ >> >>------------------------------------------------------------------------- >>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 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. 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