Alan Hewat wrote:
> I have been playing with XTALX http://fusion.stolaf.edu/chemistry/jmol/xtalx/ > using the scripts on http://www.stolaf.edu/people/hansonr/jmol/docs/ and I > have > a number of observations :-) > > 1) I am impressed by the potential of Jmol, in particular for structure > browsing > of databases. > 2) For inorganic databases like http://rruff.geo.arizona.edu/AMS/ and > http://icsd.ill.fr/ we need to use CIF files, apply symmetry operations, and > automatically draw co-ordination polyhedra. cif files are fully supported > 3) These things are now possible in Jmol, but it is not obvious how they can > be > used with minimal or zero user intervention to best represent inorganic > structures - in particular, automatic drawing of meaningful co-ordination > polyhedra. > right, this is a great challenge -- not so much just displaying for a specific model but for a general description of a database full of structures. I'm not sure it's a solvable problem. But I think you can come very close. > The AMS drawings illustrate 3). For testing purposes, I have put a simple > example of a CIF file for the YBa2Cu3O7 superconductor on > http://icsd.ill.fr/y1237.cif I would like to be able to set up Jmol so that > it > would automatically illustrate the co-ordination of all atoms to other atoms > (usually oxygen) within a given distance. In the case of Y123 it should > automatically draw Cu with square planar oxygen co-ordination plus other Cu > with > pyramidal oxygen co-ordination (see: > http://www.ill.fr/dif/3D-crystals/superconductors.html ) so beautiful! I tried to rotate them! :) My first question is, did you produce these "by hand" or did you just pull them from a database and they appeared this way? (My guess is that it took some work.) My point is simply that we may be setting an unattainable goal. Certainly you can get Jmol to do these essentially identically to what you see there in the VMRL. Hmm, but automatically? Perhaps a reasonable alternative is to deliver a structure and just enough user-ineractive functionality so that the user can build the polyhedra as he/she sees fit. This might be quite valuable and doable. > > Instead XTALX draws bonds from the central atom, (which is chemically > meaningless) and I can't see how I could write Jmol commands to pick out the > real co-ordination and draw meaningful polyhedrae. On the other hand, I was > able > to automatically construct SiO4 tetrahedrae for zeolites, which is very > useful. You just aren't familiar with the polyhedra syntax. But I also see that I messed up with polyhedra in 10.x.16; I've uploaded a revision fixing that. Bob Hanson Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein 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
