From: Karl O. <obe...@me...> - 2007-09-28 13:50:05
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I have been thinking about the same ideas. It would be useful to have only one ramachandran frame in many situations, but I also have in mind some uses in which you would need more that one plot frame. I would like to be able to make plots for two different proteins, and after viewing them separately show them combined. This brings us to the color issue. There is good reason to have a default of 'color structure' (at present time it seems like it is not doing this consistently), but I can think of situations in which one would want to change the color to something else. The above example of combining two different plots would be one illustration. Karl >>> Bob Hanson <ha...@st...> 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 <ha...@st...> 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: obe...@me... > > 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 > >Jmo...@li... > >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 > Jmo...@li... > 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 >Jmo...@li... >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 Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-users |