Bob,
I am trying to read an OBJ file created by 3dt into the Jmol application.
However I cannot get it to work. I get the following error message
$ load OBJ::FAU.obj
script ERROR: unrecognized file format type OBJ
----
load >> "OBJ::FAU.obj" <<
The beginning of the file looks like this
mtllib FAU.mtl
o tile001
g kind002
v 0,323663 0,530359 0,071414
v -0,384936 0,217535 -0,473113
v -1,093535 0,530359 0,071414
v -1,093535 0,803098 -0,700011
v -0,384936 1,115922 -0,155485
v 0,323663 0,803098 -0,700011
v -0,384936 0,939468 -1,085724
v -0,384936 0,393989 0,457126
v 0,324652 0,103367 -0,078945
v 0,546008 0,234179 -0,443000
v 0,099338 0,400845 0,437734
What am I doing something wrong? I am using Jmol.jar of 14.2.4 of Aug 3, 2014
Thanks
Christian
On 24. Sep, 2014, at 10:49, Brian McMahon <[email protected]> wrote:
> 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 ([email protected]) and
> Vladislav Blatov ([email protected]) 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: [email protected]
> 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 <[email protected]> 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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