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<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Dear Antanas<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Thank you for getting back, and updating me on the situation. I just happened to spot this entry by chance. It just happened to be the latest update when I checked the COD site.
Sadly I have no automatic checking procedure for this sort of thing!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Best Regards<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Bob<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Antanas Vaitkus <antanas.vaitkus90@gmail.com>
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<b>Sent:</b> 18 August 2025 21:47<br>
<b>To:</b> McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking@stfc.ac.uk><br>
<b>Cc:</b> cod-bugs@ibt.lt<br>
<b>Subject:</b> Re: [Cod-bugs] PubChem link<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Dear Robert,<o:p></o:p></p>
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<p class="MsoNormal">Thank you for reporting this. We will address this the next time<o:p></o:p></p>
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<p class="MsoNormal">we sync with PubChem by either updating or retracting the entry.<o:p></o:p></p>
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<p class="MsoNormal"><br>
Unfortunately, there are very likely many more such errors as there are<br>
too many entries to check by hand thus resorting to less precise automated<br>
linking (see paper [1] for more details). We do run several automated data<br>
quality checks to weed out the obviously incomplete structures, however, this<br>
one seems to have slipped past our filters. Normally, we would expect the crystal<br>
summary formula to include the missing H2O moieties, i.e. we expect it to<br>
provide the idealised crystal formula, however, the original depositor might have<br>
been following different conventions and simply calculated the formula only from<br>
the resolved atoms. <o:p></o:p></p>
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We would be grateful if you could report any other such discrepancies you notice<o:p></o:p></p>
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<p class="MsoNormal">in the COD x PubChem linkage.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Also, did you detect this error accidentally or were there any automated checks<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">involved? Maybe we could also include those in our workflow.<br>
<br>
[1] <a href="https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00780-2">
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00780-2</a><o:p></o:p></p>
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<p class="MsoNormal">Sincerely,<o:p></o:p></p>
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<p class="MsoNormal">Antanas<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, 18 Aug 2025 at 20:43, Robert McMeeking - STFC UKRI <<a href="mailto:robert.mcmeeking@stfc.ac.uk">robert.mcmeeking@stfc.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I have noticed the recent additions of PubChem links – good work.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I happened to look at COD 1529982. This is the structure of KI(H2O)2, but the coordinates of the H2O moiety have not been located. This links is to the PubChem KI entry. The links
both ways are a bit misleading!<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Best Regards<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Bob<o:p></o:p></p>
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<p class="MsoNormal">_______________________________________________<br>
Cod-bugs mailing list<br>
<a href="mailto:Cod-bugs@lists.crystallography.net" target="_blank">Cod-bugs@lists.crystallography.net</a><br>
<a href="http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs" target="_blank">http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs</a><o:p></o:p></p>
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<span class="gmailsignatureprefix">-- </span><o:p></o:p></p>
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<p class="MsoNormal">Antanas Vaitkus,<o:p></o:p></p>
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<p class="MsoNormal">Vilnius University,<br>
Life Sciences Center,<br>
Institute of Biotechnology,<br>
room C521, Saulėtekio al. 7,<br>
LT-10257 Vilnius, Lithuania<o:p></o:p></p>
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