On 18-3-2006 11:50, Dave Barthelmy wrote:
Hi Miguel,
Thanks for the advice on using .cif format. I can use the .cif format
rather than the .pdb format.
HOWEVER
Raw .cif files for minerals only contain information on the empirical
formula. Halite (rock salt) is NaCl. The .cif file for Halite only contains
two atoms, Na, and Cl and the jmolapplet depiction of halite shows the 2
atoms which look "incomplete" and do not represent the mineral structure.
What Jmol needs is to be able to take the symmetry operators and "pack" the
unit cell with more NaCl elements to illustrate the cubic array.
The following example illustrates this "packing" ability. I used Mercury to
generate the .cif files.
1. Raw cif of Diopside http://www.webmineral.com/jmol/raw.html
2. Expanded cif of Diopside http://www.webmineral.com/jmol/global.html
3. 2x Expanded cif of Diopside http://www.webmineral.com/jmol/global1.html
This is the reason why I can't use the raw cif files.
This is a "problem" for all file types that represent crystal
structures. Only the asymmetric unit is present; if you want to
visualize the packing in one or more unit cells then some program has to
apply the needed symmetry operators for the space group. Jmol is not yet
capable of generating the symmetry-related atoms; the necessary
ingredient of a programmer with java knowledge and crystallographic
symmetry understanding and time hasn't been available.
Rich
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