Brian, which of these appeal to you? http://skuld.bmsc.washington.edu/raster3d/html/rastep_options.gif
Can we use PDB format? http://nist.rcsb.org/robohelp/files_formats/structures/pdb/coordinate_file_description/anisou.htm I see 1AL4 has these codes, so I could start with that. What I need is a primer on how to translate the U matrix information to axes a, b, and c of the drawn thermal ellipsoid. Bob [EMAIL PROTECTED] wrote: >On Mon, April 14, 2008 9:28 am, Bob Hanson wrote: > > >>Brian, I would love to get this into Jmol. I think we can do a fabulous >>job of it, but I need to understand how thermal ellipsoids are >>designated in common file formats and how one would suggest depicting >>them (with the quarter-segment left out?). I did look into this a while >>back, but the designations were just too confusing for me. Currently we >>can draw ellipsoids with axes a, b, c of the form |a| = |b| != |c|. If >>we need |a| != |b| != |c|, that will be more of a challenge but not out >>of the question. >> >> > >I'd suggest using the full ellipsoid with equatorial lines rather than >making octant-removed versions. The full ellipsoid will draw faster and, >at the sizes and resolution used for on-screen drawings the >octant-removed style doesn't look so good. > >A very important option to have available is the ability to set H atoms to >spheres that are of an "artistic" size rather than the size of the B value >in the file. > >Rich > >------------------------------------------------------------------------- >This SF.net email is sponsored by the 2008 JavaOne(SM) Conference >Don't miss this year's exciting event. There's still time to save $100. >Use priority code J8TL2D2. >http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone >_______________________________________________ >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 the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
