Re: [Jmol-users] Symmetry error when loading quartz.cif

[Robert H. <ha...@st...>]

Julian, it's a bug in the CIF reader. A fixed version is at

http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip

Bob


ps; The basic problem, for the record, was this: There are two CIF terms
that introduce symmetry operators: _space_group_symop_operation_xyz, and
_symmetry_equiv_pos_as_xyz. Well, Jmol is supposed to read both of those,
but it has always only read the second because of a bug --  the first was
listed as "space_group..." rather than "_space_group". For whatever reason,
all the CIF files I have for samples use _symmetry_equiv..., so this passed
unnoticed for, ahem, 4 years. But the AMS site now uses _space_group... and
the symmetry operations were not being read properly.

Bob


On Fri, Oct 22, 2010 at 4:49 AM, Julian Mecklenburgh <
jul...@ma...> wrote:

>  Hi,
>
> I am fairly new to using Jmol and find it great tool for showing undergrad
> students 3D images of crystal structure.
>
> I have found that when I load a cif file of quartz using the following
> command:
>
> load /*file*/ "quartz.cif" {3 3 3};
>
> I do not get the correct structure. Jmol seems to put Si where there should
> be oxygens so there are not 4 oxygens surrounding each silicon. The cif file
> is from the American mineralogists crystal structure database and I checked
> that it loaded fine in crystal maker and it does. So there seem to be
> nothing wrong with the file. Any help would be greatly appreciated.
>
> Thanks
> Julian
> --
> Julian Mecklenburgh
> School of Earth, Atmospheric and Environmental Sciences
> Williamson Building
> The University of Manchester
> Manchester M13 9PL
> U.K.
> Tel: +44 161 275 3821
>       +44 161 275 3945
> Fax: +44 161 275 3947
> email:  jul...@ma...
> Web:  www.seaes.manchester.ac.uk/staff/Julian.Mecklenburgh
>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900