[Cod-bugs] COD duplication error

[Kazuki Komatsu]

Dear Antanas,

Many thanks for your advise for sorting out my problem.
I managed to deposite with the code of suboptional  as you suggested (it 
is once rejected, probably _cod_suboptimal_structure was automatically 
deleted? In the edit section, I added the code again and finally 
accepted) , and successfully allocated as entries 1566716.

Thank you again for your kind advise, and appreciate for your effort to 
manage this great database!

Best regards,

Komatsu


Antanas Vaitkus wrote on 2022/03/25 21:16:
> 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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