Alan Hewat wrote: >Great work Bob. Difficult to keep up with you. But your server: >http://www.chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.jar >(even when I remove the superfluous "www" :-) seems to have reverted to a >version of 28 slightly earlier than the one I had earlier, and I couldn't >find 29 with the features shown on your new.htm page. > hmm. Strange. Thought I just updated that. OK.
>BTW, Firefox tends >to hang on new.htm and MSIE spends a lot of time with its fancy phishing >filter; in the absence of understanding I turned it off :-) > > > I wonder what that is all about. >Now about the ellipsoid display. Dot surfaces indicating probability is a >great idea even if it gets a little confusing when ellipsoids overlap. OK, >one can use ellipsoidFill which contains more information than footballs >dotted or plain, but I still miss the old football option that you already >show in fig.1 of >http://chemapps.stolaf.edu/jmol/docs/examples-11/img/ellipsoids.jpg >maybe with an option for the black ellipse lines on/off. > >Yes, footballs can be done with other apps like Mercury, but Mercury is >not really made for inorganic structures; jmol has become uniquely >powerful there, with its polyhedra, isosurfaces etc and now anisotropic >temperature factors. For such small structures, solid surfaces for Uij, >like your very attractive isosurfaces, should perhaps not take too long? > > > No, not long. It's done. I woke up this morning with the solution and worked on it after classes today. We now have: set ellipsoidAxes on/off set ellipsoidArcs on/off set ellipsoidBall on/off set ellipsoidFill on/off set ellipsoidDots on/off ARCS show the equator lines; AXES show axes; BALL gives the standard ellipsoid FILL+ARCS gives the elliptical intersecting planes FILL+BALL gives the cutout octant DOTS gives a twinkling probability ellipsoid You can mix and match, but DOTS and any of FILL/BALL/ARCS are incompatible, and if you turn everything off, you still get AXES. So that should be plenty of options! I'm uploading now. Files should appear soon in http:chemapps.stolaf.edu/jmol/docs/examples-11 Bob >I will take a look at your x4 scale factor, but as you say it's probably >the 1/2 squared left out in the definition of Uij, that I'm sure Mercury >has right. Not too important compared to the relative magnitudes and >directions of the ellipsoid axes. > > > ok, please do check that. It's important enough that I don't want to have it wrong. -- 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
