Bob, Thermal ellipsoids were actually on my future list of questions to you :-) They are the amplitudes of thermal vibration for each atom, and in general this is anisotropic, hence ellipsoids rather than spheres. You can see how they are drawn for a CIF file if you download Mercury: http://www.ccdc.cam.ac.uk/products/csd_system/mercury/ Load a CIF file, then right-mouse-button click and choose Styles/Ellipsoids Mercury understands symmetry, but not polyhedra, being made for organics.
It's a bit late here for me to go into details, but Uii are represented by the lengths of the ellipsoid axes, and the cross terms Uij determine the orientation of these axes w.r.t. the cell axes. Uij for a given atom must of course conform to the symmetry position of that atom. It would indeed be very useful to be able to represent these "anisotropic thermal vibration amplitudes" for both organic and inorganic structures. They show at a glance interesting vibrational modes eg in a perovskite structure ABO3 particular modes of vibration condense (freeze in) resulting in structural phase transitions. I will see if I can dig up a description that might allow you to code this. Alan. PS I've done some more tweaking in http://icsd.ill.fr/ and added a print structure button (useful but not publication quality :-) Bob Hanson said: > Alan, just a thought. > > Any chance Jmol could do something with these? > > _atom_site_aniso_label > _atom_site_aniso_type_symbol > _atom_site_aniso_U_11 > _atom_site_aniso_U_22 > _atom_site_aniso_U_33 > _atom_site_aniso_U_12 > _atom_site_aniso_U_13 > _atom_site_aniso_U_23 > > like display ellipsoids? I read: > > Definition > > These are the standard anisotropic atomic displacement > components in angstroms squared which appear in the > structure factor term: _____________________________________________________________ Dr Alan Hewat, ILL Grenoble, FRANCE <[EMAIL PROTECTED]>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm _____________________________________________________________ Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
