[Cod-bugs] Some structures published in Acta Cryst. E are missing in COD

[Koichi Kitahara]

Dear  Saulius,

Thank you for re-running the script to add our structures to COD.
I would like to report If I find other missing structures.

Best regards,
Koichi Kitahara

On Tue, Nov 28, 2023 at 4:58 PM Saulius Gražulis <grazulis at ibt.lt> wrote:

> Dear Koichi,
>
> thank you very much for your e-mail and for the valuable bug report!
>
> On 2023-11-25 03:28, Koichi Kitahara wrote:
> >
> > I found that some structures published in Acta Cryst. E are missing in
> COD.
> > Are there any criteria for structures to be available in COD,
>
> The only exclusion criteria for structures published in reputable
> peer-reviewed publications is that we do not want, as a rule,
> theoretical structures into the COD – such structures should go into the
> TCOD [2]. Even then sometimes theoretical structures end up in the COD
> if they are not recognised as theoretical, and are only sorted later.
>
> So any missing structure can be considered a bug in the COD.
>
> > ... or are
> > there some bugs in automatic extraction routines of COD?
>
> You are right, there was a transient problem in the deposition pipeline
> (connection to port 80 timed out). Such timeouts happen when the system
> is overloaded with external connections; we are working to find a
> solution for this problem.
>
> Meanwhile, I have re-run the deposition scripts manually and the
> structures are in the COD :) [3]
>
> > In particular, I'm wondering if our structures [1] will be available in
> > COD in near future or not.
>
> We are trying to get structures into the COD as soon as possible. I'am
> sorry for this delay in the publication of the structures, this was a
> glitch which we overlooked.
>
> Meanwhile, we would be grateful if you report any other such issues of
> the missing published structures. While we do have the deposition logs
> for these failures, we lack manpower to address these issues quickly;
> thus the reports from the COD users are very helpful :)
>
> Sincerely yours,
> Saulius
>
> Refs.:
>
>  > [1] https://doi.org/10.1107/S2056989023008393
> <https://doi.org/10.1107/S2056989023008393>
>
> [2] The Theoretical Crystallography Open Database (TCOD).
> https://www.crystallography.net/tcod/
>
> [3] Kitahara, Koichi; Takakura, Hiroyuki; Iwasaki, Yutaka; Kimura,
> Kaoru. Crystal structures of five compounds in the
> aluminium-ruthenium-silicon system.     Acta crystallographica Section E,
> Crystallographic communications (2023) 79(10), 946--951.
>
> http://www.crystallography.net/cod/2312358.html
> http://www.crystallography.net/cod/2312359.html
> http://www.crystallography.net/cod/2312360.html
> http://www.crystallography.net/cod/2312361.html
> http://www.crystallography.net/cod/2312362.html
> [accessed 2023-11-28T09:50+02:00].
>
> --
> Dr. Saulius Gražulis
> Vilnius University, Life Science Center, Institute of Biotechnology
> Saulėtekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania)
> phone (office): (+370-5)-2234353, mobile: (+370-684)-49802,
> (+370-614)-36366
>
>
> --
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>

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