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

[Saulius Gražulis]

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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