OK, Alan, that's great. I look forward to hearing about your user feedback.
Rendering. I think you are going to like this. It is NOT your typical football rendering -- but I will argue that you can get that with other programs, and maybe Jmol should do better. Football dots. Pointilist footballs? The dots that form the football twinkle with model manipulation -- suggestive, perhaps of their probabilistic reference. You can set how many dots -- the default is 200, but 500 looks pretty cool, I think. (And I've hit a brick wall trying to figure out how to efficiently calculate the ellipse created by the intersection of a plane with an arbritrary ellipsoid.) So, here you go... see http://www.chemapps.stolaf.edu/jmol/docs/examples-11/new.htm and http://www.chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.jar # new features for ellipsoid rendering [default settings in brackets]: # # set ellipsoidAxes [false] # set ellipsoidArcs [false] # set ellipsoidFill [false] # set ellipsoidDots [true] # set ellipsoidDotCount [200] # # [dots|stars|spacefill] ADPMIN [percent] # [dots|stars|spacefill] ADPMAX [percent] # The combination I think is really interesting -- to my eye FAR more informative than a football -- is this: set ellipsoidDots off set ellipsoidFill on wireframe on;spacefill ADPMIN 50; ellipsoids 50 What this gives is a nice-looking solid sphere at the 50% level for the minimium displacement (the shortest axis) and elliptical planes slicing out of it in the directions of the other two axes. I can very quickly see the problems with mega displacements, and I can detect slight differences in the two minor axes as well. Something to think about. I still need someone to take a very close look at the 50, 75, 100% sizes and tell me if I have that right. Does it scale properly? There's a factor of 4 there I had to throw in to make it match Mercury, but I don't know why I had to do that. Doesn't surprise me -- I probably left it out of the U-->B conversion or something like that. I've changed the temperature to be (U11 * U22 * U33)^(0.333) This is only set if the atomic Bfactors are NOT set. Atomic Bfactors take precedence (for compatibility with previous versions). Oh, and by the way, when you set spacefill ADPMIN 100 the atom's radius parameter reads off the minimum axis length. spacefill ADPMIN 100 print {*}.radius # average print {*}.radius.min # minimum print {_O}.radius.max # maximum for oxygen select {radius > 0.4}; color yellow;label "OH,OH" I think this may have potential. *Bob * -- 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
