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Questions about CIF files

  • Subject: Questions about CIF files
  • From: =?utf-8?q?S=C3=A9bastien_Le_Roux_via_cif-developers?=<cif-developers@xxxxxxxxxxxxxxxx>
  • Date: Tue, 27 May 2025 11:54:35 +0200
  • Cc: =?UTF-8?Q?S=C3=A9bastien_Le_Roux?= <sebastien.leroux@xxxxxxxxxxxxxxxx>
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Hello everyone,
my name is Sébastien Le Roux: https://www.ipcms.fr/sebastien-le-roux/
I am the developer of the atomes software: https://atomes.ipcms.fr/
Among other things atomes can be used to read CIF files, and recently a co-worker of mine
came across an example case that got me thinking, and I would really appreciate your advise to know what to do.

Here is the paper, and the corresponding CIF file I am asking your opinion about:

 https://journals.iucr.org/paper?S0108768105034014

The CIF contains several set of atomic coordinates, that corresponds to a chemical reaction,
that is a transformation of configuration of a molecule in the same crystalline structure, space group, etc.
Each configuration describing a step in this chemical reaction, with the proportion of each conformation
being described by the occupancy field, or at least that is what I understand and want to figure out.
I would like to ask you opinion to know I understand this correctly.
Assuming that is correct and if I consider the CIF file as as trajectory describing the chemical reaction,
then to build this trajectory, for each set of atomic coordinates, I would need to: 
 - build a crystal respecting the proportion (occupancy) of each conformation
 - build a (super)crystal large enough to so that even the lowest occupancy would lead to a cell being filled.
 - ensure that the size of the crystal is the same for each step, and therefore that the lowest occupancy
 in the overall CIF file dictate the size of the final crystal.

I would really appreciate your opinion of this, since I am not familiar with this kind of CIF files.
Is this interpretation based on the occupancy field correct ?
If that is the case then is there any other information in the CIF file that would help me separate atomic coordinates other than the occupancy ?
Also it this type of CIF file common ? (so far I tried unsuccessfully to find other examples to verify my hypothesis).

Finally, and on a different subject, would you know what to do to add atomes to the visualization tools that can read CIF files,
on this page: https://www.iucr.org/resources/cif/software

Thanks in advance for your help.
Best regards.

Sébastien Le Roux
-- 
===========================================================
Dr. Sébastien Le Roux
Ingénieur de Recherche CNRS
Institut de Physique et Chimie des Matériaux de Strasbourg
Département des Matériaux Organiques
23, rue du Loess
BP 43
F-67034 Strasbourg Cedex 2, France
E-mail: [email protected]
Webpage: https://www.ipcms.fr/sebastien-le-roux/
ATOMES project: https://atomes.ipcms.fr/
RINGS project: http://rings-code.sourceforge.io/
ISAACS project: http://isaacs.sourceforge.io/
Phone: +33 3 88 10 71 58
===========================================================

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