Hi Bob, Christian
This is a very timely discussion. I've recently returned from
the first European Crystallography School in Pavia, where I
talked with Davide Proserpio (davide.proser...@unimi.it) and
Vladislav Blatov (bla...@samsu.ru) about this. I'll copy them
into this message. Their program TOPOS
(http://www.topos.samsu.ru/starting.html) is perhaps the most
intensively maintained and developed such software at the moment.
It could be helpful if Jmol were able to read and render output
files from TOPOS.
However, Davide is also interested in using CIF as an existing
standard exchange format. (Some of these tilings are generated
by mathematical applications that are solely interested in
topology, for which a very simple format is appropriate; but
others do represent or model real crystal structures.) We
figure that it would be helpful for Jmol to have a mode where
it rendered only bonds in a CIF that had a specific flag set,
something like
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_1
_geom_bond_site_symmetry_2
_topos_geom_bond_publ_flag
X1 X2 1.342(4) 1_555 1_555 yes
X1 X2 1.439(3) 1_555 2_565 yes
X2 X3 1.512(4) 1_555 1_555 no
Perhaps we could follow this up off-list?
Best wishes
Brian
_________________________________________________________________________
Brian McMahon tel: +44 1244 342878
Research and Development Officer fax: +44 1244 314888
International Union of Crystallography e-mail: b...@iucr.org
5 Abbey Square, Chester CH1 2HU, England
On Tue, Sep 23, 2014 at 11:17:12AM +0200, Christian Baerlocher wrote:
> Dear Bob,
>
> You are of course quite right, there is no SiO2 molecule, because quartz and
> all its polymorphs are ?periodic nets?. You have to select a ?cluster? and to
> make it neutral you would have to add terminal OH groups.
>
> This is a problem we face also in zeollite chemistry (many of them are
> polymorphs of SiO2) and a number of attempts had been made to define suitable
> clusters that describe a structure. So far the best approach for periodic
> nets seems to be that of "natural tilings?, defined and described by V. A.
> Blatov, O. Delgado-Friedrichs, M. O'Keeffe & D. M. Proserpio, Acta
> Crystallogr. A 63, 418-425 (2007). These natural tilings are further
> discussed by N. Anurova, V. A. Blatov, G. D. Ilyushin and D. M. Proserpio, J.
> Phys. Chem. C 114, 10160-10170 (2010).
>
> You can see examples of such tilings on our zeolite website. For example, for
> the natural zeolite faujasite in
> http://izasc.ethz.ch/fmi/xsl/IZA-SC/Tilings/FAU.pdf
>
> Its framework of faujasite can be viewed with JSmol on
> http://izasc.ethz.ch/fmi/xsl/IZA-SC/ftc_3d_JSmol.php
>
> These natural tilings have been done for all zeolites.
>
> I am not sure, if this is what Hans Horn was looking for, but it would
> certainly be nice if Jmol could display such drawings ;-)
>
> Thanks and best wishes
>
> Christian
>
>
>
> On 20 Sep 2014, at 04:24, Robert Hanson <hans...@stolaf.edu> wrote:
>
> > Well, I think it is an interesting request. Help me define what the idea is
> > a bit more, and I can see what I can do. Given a few choice examples, how
> > would you define your request exactly?
> >
> > For example, we have quartz (SiO2):
> > http://chemapps.stolaf.edu/jmol/simple2.htm?load%20jsmol/data/quartz.cif%20{1%201%201}
> >
> > In this unit cell we have
> >
> > Si 1 + 4(1/2) = 3 atoms
> > O 6 atoms
> >
> > But which three atoms would you choose to represent the model for "SiO2"?
> > Is it always possible to identify such a subset? Some cases probably
> > involve multiple options, and they are not equivalent. For example, in this
> > case, there is not a perfect tetrahedron around that Si atom. So picking
> > different O atoms would give different structures for the formula unit.
> > Which one would be the correct one to load? Sounds very challenging to me.
> >
> > Bob
> > ?
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