From robert.mcmeeking at stfc.ac.uk Mon Aug 18 20:43:06 2025 From: robert.mcmeeking at stfc.ac.uk (Robert McMeeking - STFC UKRI) Date: Mon, 18 Aug 2025 17:43:06 +0000 Subject: [Cod-bugs] PubChem link Message-ID: Hi I have noticed the recent additions of PubChem links - good work. 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! Best Regards Bob -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From antanas.vaitkus90 at gmail.com Mon Aug 18 23:46:58 2025 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Mon, 18 Aug 2025 23:46:58 +0300 Subject: [Cod-bugs] PubChem link In-Reply-To: References: Message-ID: Dear Robert, Thank you for reporting this. We will address this the next time we sync with PubChem by either updating or retracting the entry. Unfortunately, there are very likely many more such errors as there are too many entries to check by hand thus resorting to less precise automated linking (see paper [1] for more details). We do run several automated data quality checks to weed out the obviously incomplete structures, however, this one seems to have slipped past our filters. Normally, we would expect the crystal summary formula to include the missing H2O moieties, i.e. we expect it to provide the idealised crystal formula, however, the original depositor might have been following different conventions and simply calculated the formula only from the resolved atoms. We would be grateful if you could report any other such discrepancies you notice in the COD x PubChem linkage. Also, did you detect this error accidentally or were there any automated checks involved? Maybe we could also include those in our workflow. [1] https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00780-2 Sincerely, Antanas On Mon, 18 Aug 2025 at 20:43, Robert McMeeking - STFC UKRI < robert.mcmeeking at stfc.ac.uk> wrote: > Hi > > > > I have noticed the recent additions of PubChem links ? good work. > > > > 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! > > > > Best Regards > > > > Bob > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. > _______________________________________________ > Cod-bugs mailing list > Cod-bugs at lists.crystallography.net > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs > -- Antanas Vaitkus, Vilnius University, Life Sciences Center, Institute of Biotechnology, room C521, Saul?tekio al. 7, LT-10257 Vilnius, Lithuania -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From robert.mcmeeking at stfc.ac.uk Tue Aug 19 11:27:37 2025 From: robert.mcmeeking at stfc.ac.uk (Robert McMeeking - STFC UKRI) Date: Tue, 19 Aug 2025 08:27:37 +0000 Subject: [Cod-bugs] PubChem link In-Reply-To: References: Message-ID: Dear Antanas 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! Best Regards Bob From: Antanas Vaitkus Sent: 18 August 2025 21:47 To: McMeeking, Robert (STFC,DL,SC) Cc: cod-bugs at ibt.lt Subject: Re: [Cod-bugs] PubChem link Dear Robert, Thank you for reporting this. We will address this the next time we sync with PubChem by either updating or retracting the entry. Unfortunately, there are very likely many more such errors as there are too many entries to check by hand thus resorting to less precise automated linking (see paper [1] for more details). We do run several automated data quality checks to weed out the obviously incomplete structures, however, this one seems to have slipped past our filters. Normally, we would expect the crystal summary formula to include the missing H2O moieties, i.e. we expect it to provide the idealised crystal formula, however, the original depositor might have been following different conventions and simply calculated the formula only from the resolved atoms. We would be grateful if you could report any other such discrepancies you notice in the COD x PubChem linkage. Also, did you detect this error accidentally or were there any automated checks involved? Maybe we could also include those in our workflow. [1] https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00780-2 Sincerely, Antanas On Mon, 18 Aug 2025 at 20:43, Robert McMeeking - STFC UKRI > wrote: Hi I have noticed the recent additions of PubChem links ? good work. 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! Best Regards Bob -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ Cod-bugs mailing list Cod-bugs at lists.crystallography.net http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs -- Antanas Vaitkus, Vilnius University, Life Sciences Center, Institute of Biotechnology, room C521, Saul?tekio al. 7, LT-10257 Vilnius, Lithuania -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From malikashtar245 at gmail.com Thu Aug 21 08:04:05 2025 From: malikashtar245 at gmail.com (Malik Ashtar) Date: Thu, 21 Aug 2025 13:04:05 +0800 Subject: [Cod-bugs] (no subject) Message-ID: Dear COD Support Team, I hope this message finds you well. I am currently experiencing an issue while searching for materials on the Crystallographic Open Database (COD) website. When I conduct a search for a material, multiple pages appear. However, when attempting to switch to a different page (if the material is not found on the first page), the page becomes blank, and I am unable to view any results. I have tried accessing the site from different browsers and devices, but the issue persists. Could you kindly assist me with resolving this problem, or let me know if there is an ongoing issue with the site that may be causing this behavior? Thank you for your attention to this matter. I look forward to your assistance. Best regards, Dr. Malik Ashtar IOP,CAS -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From antanas.vaitkus90 at gmail.com Thu Aug 21 15:40:20 2025 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Thu, 21 Aug 2025 15:40:20 +0300 Subject: [Cod-bugs] (no subject) In-Reply-To: References: Message-ID: Dear Malik Ashtar, I confirm that I can reproduce the described behaviour. This seems like a temporary issue on our side due to the activity of malicious web bots. We have resolved the issue for now, but it is quite likely to reoccur in the future. We will look into finding a more permanent solution. Sincerely, Antanas On Thu, 21 Aug 2025 at 09:22, Malik Ashtar wrote: > Dear COD Support Team, > > I hope this message finds you well. I am currently experiencing an issue > while searching for materials on the Crystallographic Open Database (COD) > website. When I conduct a search for a material, multiple pages appear. > However, when attempting to switch to a different page (if the material is > not found on the first page), the page becomes blank, and I am unable to > view any results. > > I have tried accessing the site from different browsers and devices, but > the issue persists. Could you kindly assist me with resolving this problem, > or let me know if there is an ongoing issue with the site that may be > causing this behavior? > > Thank you for your attention to this matter. I look forward to your > assistance. > > Best regards, > > Dr. Malik Ashtar > > IOP,CAS > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. _______________________________________________ > Cod-bugs mailing list > Cod-bugs at lists.crystallography.net > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs > -- Antanas Vaitkus, Vilnius University, Life Sciences Center, Institute of Biotechnology, room C521, Saul?tekio al. 7, LT-10257 Vilnius, Lithuania -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: