Brian McMahon wrote: >Dear Bob > >At first glance, tested against a number of Acta Cryst. C structures >with relatively large or elongated ellipsoids, this is looking very >nice indeed. > >So far the only issue I have come across is the logic of handling >mixed isotropic/anisotropic refinements; in the CIF > http://scripts.iucr.org/cgi-bin/sendcif?gd3149sup1 >there are a number of atoms (O43, O53) which have been refined >isotropically and are listed in the main atom list with their >values of _atom_site_U_iso_or_equiv. They don't appear in the >separate list of atoms with anisotropic Uij values. So Jmol >doesn't display them at all in the "ellipsoid" mode. I guess >they should appear as suitably scaled spheres, perhaps with some >indication that they are U_equivalent's; or perhaps with a mode >that can switch on/off "ellipsoid" displays for isotropically >refined atoms. > > I'd like to be translate those to Uij values. Can you find out how to do that? I see
http://www.iucr.org/iucr-top/cif/cif_core/definitions/Cdata_atom_site_U_iso_or_equiv.html but... >My editorial colleagues are happy with the idea of using the >"temperature" colour scheme in association with these ellipsoids, >and in these examples that also works well. > > > Note that I am defining temperature as (U11 + U22 + U33)/3.0 * 100 If this is not correct, please let me know. (I can't find where I read that, and I don't know if I remember it correctly.) >I'll build some options arising from this into our enhanced >figures toolkit and encourage the technical editors here to >experiment some more. > > > great. >The drop-down menu will benefit from having some of this functionality >added. An obvious extension would be to add "displacement ellipsoids" >to the list of Style>Scheme, but it might also be useful to have a >menu option to select between different styles of representation (axes, >footballs, etc.) when these become available. > > > right.... >Thank you very much for the work you've put into this: for our >small-molecule applications this will enormously increase the >impact of Jmol enhanced figures! > > > terrific. >Best wishes >Brian >_________________________________________________________________________ >Brian McMahon tel: +44 1244 342878 >Research and Development Officer fax: +44 1244 314888 >International Union of Crystallography e-mail: [EMAIL PROTECTED] >5 Abbey Square, Chester CH1 2HU, England > > > >On Thu, Apr 17, 2008 at 02:14:06AM -0500, Bob Hanson wrote: > > >>Alright. Time to test. See >> >>http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm >>http://chemapps.stolaf.edu/jmol/docs/examples-11/ellipsoids.jpg >>http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.zip >> >>Bob >> >> >> >>Bob Hanson wrote: >> >> >> >>>Alan, Thomas, Brian, Rich, others, >>> >>>OK, progress. I have just uploaded code introducing the ELLIPSOID >>>command. All it does at this point is draw the axes. But that's enough >>>to convince me I do have the Uij --> ellipsoid axes conversion correct, >>>and that is no small achievement! The ellipsoid axes are determined by >>>first transforming the Uij to Bij, then expressing the B matrix in terms >>>of cartesian coordinates. Then solving the eigenvector problem to find >>>the rotation that sets all nondiagonal elements 0 so that the >>>characteristic equation is of the form >>> >>> a11 x^2 + a22 y^2 + a33 z^2 = constant >>> >>>For the record, this required adding a small eigenvector/eigenvalue >>>solver class (public domain, NIST - JAMA; org/jmol/symmetry/Eigen.java). >>> >>>Still to do are (a) symmetry considerations and (b) footballs. >>> >>>I hope to look at this later today. Symmetry should be no problem. I'm >>>pretty sure just have to make sure I'm multiplying matrices properly. >>>Some nice examples with different symmetries and poor data (lots of >>>anisotropy) would be helpful. Alan, do you have any BAD data??? (Feel >>>free to send it to me off line if you would prefer.) Once we have >>>symmetry, we will at least have visualizations to check. Footballs can >>>come later. >>> >>>At some point we need to confirm that the axes are the correct absolute >>>length. I think I can do footballs without isosurfaces. Tricky, though. >>>We need to find out how to draw ellipsoids in POV-Ray. We might even get >>>the POV-Ray output going first if that turns out to be a relatively easy >>>operation. >>> >>>Colors -- for now let's just stick with what Jmol can do with colors >>>already. This includes temperature, which I believe can be calculated >>>from Uij using: >>> >>>bFactor = (U11 + U22 + U33)/3 >>> >>>but I'm not 100% sure that is correct. >>> >>>Bob >>> >>> > >------------------------------------------------------------------------- >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 >Jmol-users@lists.sourceforge.net >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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
