<div dir="ltr">Dear
Saulius,<div><br></div><div>Thank you for re-running the script to add our structures to COD.</div><div>I would like to report If I find other missing structures.</div><div><br></div><div>Best regards,</div><div>Koichi Kitahara</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Nov 28, 2023 at 4:58 PM Saulius Gražulis <<a href="mailto:grazulis@ibt.lt">grazulis@ibt.lt</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Koichi,<br>
<br>
thank you very much for your e-mail and for the valuable bug report!<br>
<br>
On 2023-11-25 03:28, Koichi Kitahara wrote:<br>
> <br>
> I found that some structures published in Acta Cryst. E are missing in COD.<br>
> Are there any criteria for structures to be available in COD,<br>
<br>
The only exclusion criteria for structures published in reputable <br>
peer-reviewed publications is that we do not want, as a rule, <br>
theoretical structures into the COD – such structures should go into the <br>
TCOD [2]. Even then sometimes theoretical structures end up in the COD <br>
if they are not recognised as theoretical, and are only sorted later.<br>
<br>
So any missing structure can be considered a bug in the COD.<br>
<br>
> ... or are <br>
> there some bugs in automatic extraction routines of COD?<br>
<br>
You are right, there was a transient problem in the deposition pipeline <br>
(connection to port 80 timed out). Such timeouts happen when the system <br>
is overloaded with external connections; we are working to find a <br>
solution for this problem.<br>
<br>
Meanwhile, I have re-run the deposition scripts manually and the <br>
structures are in the COD :) [3]<br>
<br>
> In particular, I'm wondering if our structures [1] will be available in <br>
> COD in near future or not.<br>
<br>
We are trying to get structures into the COD as soon as possible. I'am <br>
sorry for this delay in the publication of the structures, this was a <br>
glitch which we overlooked.<br>
<br>
Meanwhile, we would be grateful if you report any other such issues of <br>
the missing published structures. While we do have the deposition logs <br>
for these failures, we lack manpower to address these issues quickly; <br>
thus the reports from the COD users are very helpful :)<br>
<br>
Sincerely yours,<br>
Saulius<br>
<br>
Refs.:<br>
<br>
> [1] <a href="https://doi.org/10.1107/S2056989023008393" rel="noreferrer" target="_blank">https://doi.org/10.1107/S2056989023008393</a> <br>
<<a href="https://doi.org/10.1107/S2056989023008393" rel="noreferrer" target="_blank">https://doi.org/10.1107/S2056989023008393</a>><br>
<br>
[2] The Theoretical Crystallography Open Database (TCOD). <br>
<a href="https://www.crystallography.net/tcod/" rel="noreferrer" target="_blank">https://www.crystallography.net/tcod/</a><br>
<br>
[3] Kitahara, Koichi; Takakura, Hiroyuki; Iwasaki, Yutaka; Kimura, <br>
Kaoru. Crystal structures of five compounds in the <br>
aluminium-ruthenium-silicon system. Acta crystallographica Section E, <br>
Crystallographic communications (2023) 79(10), 946--951.<br>
<br>
<a href="http://www.crystallography.net/cod/2312358.html" rel="noreferrer" target="_blank">http://www.crystallography.net/cod/2312358.html</a><br>
<a href="http://www.crystallography.net/cod/2312359.html" rel="noreferrer" target="_blank">http://www.crystallography.net/cod/2312359.html</a><br>
<a href="http://www.crystallography.net/cod/2312360.html" rel="noreferrer" target="_blank">http://www.crystallography.net/cod/2312360.html</a><br>
<a href="http://www.crystallography.net/cod/2312361.html" rel="noreferrer" target="_blank">http://www.crystallography.net/cod/2312361.html</a><br>
<a href="http://www.crystallography.net/cod/2312362.html" rel="noreferrer" target="_blank">http://www.crystallography.net/cod/2312362.html</a><br>
[accessed 2023-11-28T09:50+02:00].<br>
<br>
-- <br>
Dr. Saulius Gražulis<br>
Vilnius University, Life Science Center, Institute of Biotechnology<br>
Saulėtekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania)<br>
phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366<br>
<br>
<br>
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