Hi All, I am trying to render the electrostatic potential surfaces for the 20 individual amino acids, to illustrate the differences in side chain polarity. (Ultimately, I will be showing partial surfaces, over the side chains only.)
I have some mol2 files of zwitterionic amino acids containing the EPS values. The highest EPS value in each file is 0.2751 and the lowest is -0.6478 (or -0.6464, which I take to be a negligible difference). These values are for the charged amines and carboxyls, and my thought was that they would set a good absolute scale for showing the differences in polarity between the side chains. (This will be particularly important when I render the isosurface over the side chains only, otherwise I will get relative coloring that will make the nonpolar side chains look similar to polar side chains.) Using a red- white-blue color scheme, then, I expect that nonpolar side chains such as valine should come out with very faint red and blue, whereas charged side chains such as aspartate should have significantly deeper colorings. When I use the command isosurface colorscheme "rwb" sasurface 0.1 color range all map mep the results make perfect sense if I am looking at the surface of the entire amino acid, but once I restrict it to the side chain, the relative coloring I don't want (as above) is the result. So to force the range to be absolute, I am using the command isosurface colorscheme "rwb" sasurface 0.1 color range -0.6478 0.2751 map mep Because these are the highest and lowest values in the files, I'd expect the charged groups to show up as bright red or blue, and nonpolar areas to be faint. However, I am not getting the results I am anticipating. Aspartate's surface has only faint colors, and valine is actually a medium shade of blue. I don't get it. In response to the command above, Jmol comes back with this for Asp: color range -0.6478 0.2751; mapped data range -0.26758346 to 0.03863874 and this for Val: color range -0.6478 0.2751; mapped data range -0.19274539 to 0.16532882 What does the mapped data range refer to? The numbers seem to correspond with the colors I am seeing, but do not correspond to the eps values in the file. I've also tried using "... color absolute -0.6478 0.2751 ...", which seems to give the same effect. I've tried using fewer decimal places, and experimented with different absolute ranges, but I don't want to choose something arbitrary. Am I misunderstanding what "color range/absolute x.xxx y.yyy" should be doing? Is there a way to get the coloring for "color range all" but only show the surface for the side chains? Frieda ////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 ////////////////////////////////////// ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
