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.
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.
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 )
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.
Alan.
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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
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