[Cod-bugs] COD duplication error

[Antanas Vaitkus]

Dear Kazuki Komatsu,

You very correctly identified that the issue arose due to the fact that
both models were derived from the same data and are therefore very similar.
In the COD we handle such situations by declaring one of the structures as
optimal and the rest of them (in case there is more than one alternative
model) as suboptimal. The optimal structure is mainly chosen based on the R
factor.

In your specific case the problem could be circumvented  by adding the
following extra line to the CIF file that you are trying to deposit:

_cod_suboptimal_structure        yes

This simply declares that the deposited structure is suboptimal and
therefore can match a similar structure that is already in the COD. After
your deposition, we will further investigate the structure to evaluate if
it is actually suboptimal or optimal in regards to the existing COD
structure and update the relationships accordingly. After this, the
relationship will also become visible on the COD website. See COD entry
2100860 [1] for an example of how this looks (entry is marked as a
suboptimal structure of COD entry 2100858).

Could you please try the suggested approach and let me know if it was
successful?

[1] https://www.crystallography.net/cod/2100860.html

Sincerely,
Antanas



On Mon, 21 Mar 2022 at 08:31, Kazuki Komatsu <kom at eqchem.s.u-tokyo.ac.jp>
wrote:

> Dear COD developer team,
>
> I recently try to deposit the attached cif file to the COD. It is
> validated, but can not be allocated as a new entry due to the duplication
> to the previously deposited item 1538611.
>
> The previous entry is the same compound, based on the same data from the
> same publication, but refined as a different structure model, so that they
> should be separately regarded.
>
> Could you let me know how this should be resolved?
>
> Thank you so much for your effort to manage this issue in advance.
>
>
> Best regards,
>
>
> Kazuki Komatsu, Ph.D.
>
> Associate Prof.
> Graduate School of Science, The University of Tokyo
>
>
>
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-- 
Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saulėtekio al. 7,
LT-10257 Vilnius, Lithuania

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