Menu
▾
▴
[Jmol-users] Symmetry, bonds and polyhedra in Jmol with databases
|
From: Alan H. <he...@il...> - 2006-06-28 10:17:14
|
<html> <body> I have been playing with XTALX <a href="http://fusion.stolaf.edu/chemistry/jmol/xtalx/" eudora="autourl"> http://fusion.stolaf.edu/chemistry/jmol/xtalx/</a> using the scripts on <a href="http://www.stolaf.edu/people/hansonr/jmol/docs/" eudora="autourl"> http://www.stolaf.edu/people/hansonr/jmol/docs/</a> and I have a number of observations :-)<br><br> 1) I am impressed by the potential of Jmol, in particular for structure browsing of databases.<br> 2) For inorganic databases like <a href="http://rruff.geo.arizona.edu/AMS/" eudora="autourl"> http://rruff.geo.arizona.edu/AMS/</a> and <a href="http://icsd.ill.fr/" eudora="autourl">http://icsd.ill.fr/</a> we need to use CIF files, apply symmetry operations, and automatically draw co-ordination polyhedra.<br> 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. <br><br> The AMS drawings illustrate 3). For testing purposes, I have put a simple example of a CIF file for the YBa2Cu3O7 superconductor on <a href="http://icsd.ill.fr/y1237.cif" eudora="autourl"> http://icsd.ill.fr/y1237.cif</a> 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 <b>automatically </b>draw Cu with square planar oxygen co-ordination plus other Cu with pyramidal oxygen co-ordination (see: <a href="http://www.ill.fr/dif/3D-crystals/superconductors.html"> http://www.ill.fr/dif/3D-crystals/superconductors.html</a> )<br><br> 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.<br><br> Alan.<br> </body> <br> <div>_____________________________________________________________</div> <div>Dr Alan Hewat, ILL Grenoble, FRANCE<he...@il...>fax+33.476.20.76.48</div> <div>+33.476.20.72.13 (.26 Mme Guillermet) <a href="http://www.ill.fr/dif/AlanHewat.htm" EUDORA=AUTOURL> http://www.ill.fr/dif/AlanHewat.htm</a> </div> <div>_____________________________________________________________</div> </html> |