From raquel.portela at csic.es Mon May 19 19:34:07 2025 From: raquel.portela at csic.es (Raquel) Date: Mon, 19 May 2025 18:34:07 +0200 Subject: [Cod-bugs] Curated compilation of Raman spectroscopy databases Message-ID: <46d95637-35af-4fa7-97c7-de0c0e72dccb@csic.es> Dear Raman database manager, I would like to inform you that your database has been included in the comprehensive and curated list of openly accessible online Raman databases with information about their content and origin that we have published in Zenodo. Their FAIRness level has also been evaluated. A tab with some relevant proprietary Raman databases is also included as complementary information on the availability of Raman data. You can access it through the DOI: https://doi.org/10.5281/zenodo.15268226 This is a living document, if you contact us with your feedback it will be taken into account in the next updated version. If you want help us disseminate the resource, you may find useful this LinkedIn post . Thank you on behalf of all authors. Looking forward to hearing from you. Best reagards, Raquel Portela Re: Fwd: Sales representatives and distributors -- *Dr. Raquel Portela* Cient?fica Titular | Tenured Scientist Instituto de Cat?lisis y Petroleoqu?mica CONSEJO SUPERIOR DE INVESTIGACIONES CIENT?FICAS ? +34 915854873 (ext.) | 437516 (int.) @ raquel.portela at csic.es cid:image004.png at 01D81F8D.9BC55400https:// icp.csic.es ?C/ Marie Curie, 2, Cantoblanco. 28049 Madrid, Spain. -- 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: rs9v0l3f3uHvDhZ0.png Type: image/png Size: 6300 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ql2JEbL0LvE5yIKg.png Type: image/png Size: 454 bytes Desc: not available URL: From post at hbergwerf.nl Wed May 21 12:26:22 2025 From: post at hbergwerf.nl (Herman Bergwerf) Date: Wed, 21 May 2025 11:26:22 +0200 Subject: [Cod-bugs] Potential firewall block Message-ID: <20250521112622.0878a996@antec.nimma> Hi, I am experiencing some issues with using COD on molview.org; we are accessing the COD MySQL database and the crystallography.net cif files, but these are no longer working and we are wondering if the server we are hosting molview.org on is being blocked by the firewall. Our server IP is: 68.66.248.52 molview.org is on shared hosting without SSH access, so sadly I have very limited access for debugging this (but I can ask the support team if needed). I can imagine there were unreasonably many requests to the MySQL database coming from our server. I quite inefficiently programmed the CIF retrieval script to first check in the database if the COD record exists and has coordinates, and only after that do I attempt to download the CIF file. I can change this to just trying to download the CIF file, which should significantly reduce the load you are experiencing from molview.org Thanks, Herman Bergwerf -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From antanas.vaitkus90 at gmail.com Wed May 21 13:35:22 2025 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Wed, 21 May 2025 13:35:22 +0300 Subject: [Cod-bugs] Potential firewall block In-Reply-To: <20250521112622.0878a996@antec.nimma> References: <20250521112622.0878a996@antec.nimma> Message-ID: Dear Herman, Thank you for reaching out. Recently our servers started being routinely overwhelmed by search engine/AI platform crawler bots, therefore we had to implement a slightly stricter automatic blocking policy. Your usage does not seem to fall under this category therefore we will whitelist your server IP. Could you please let us know if this fixed the issue on your end? As for your suggestion, optimising your workflow to minimise the number of queries is always welcome (as well as pausing between several queries). However, in this case the CIF download itself is probably the more expensive query (could please provide some specifics on how you download the files?). You are welcome to continue downloading COD files using your current approach, but I would also recommend looking into downloading the entire COD dataset and serving it from a local copy (see https://wiki.crystallography.net/howtoobtaincod/). Specifically, the Subversion or rsync approaches would be the easiest to keep in sync and up to date. Sincerely, Antanas On Wed, 21 May 2025 at 12:28, Herman Bergwerf wrote: > Hi, > > I am experiencing some issues with using COD on molview.org; we are > accessing the COD MySQL database and the crystallography.net cif files, > but these are no longer working and we are wondering if the server we > are hosting molview.org on is being blocked by the firewall. > > Our server IP is: 68.66.248.52 > > molview.org is on shared hosting without SSH access, so sadly I have > very limited access for debugging this (but I can ask the support team > if needed). > > I can imagine there were unreasonably many requests to the MySQL > database coming from our server. I quite inefficiently programmed the > CIF retrieval script to first check in the database if the COD record > exists and has coordinates, and only after that do I attempt to > download the CIF file. I can change this to just trying to download the > CIF file, which should significantly reduce the load you are > experiencing from molview.org > > Thanks, > Herman Bergwerf > > > -- > 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 mehmet.giritli at stfc.ac.uk Fri May 23 13:51:18 2025 From: mehmet.giritli at stfc.ac.uk (Mehmet Giritli - STFC UKRI) Date: Fri, 23 May 2025 10:51:18 +0000 Subject: [Cod-bugs] Optimade API returns empty results for SMILES query, while web interface works properly for the same SMILES value Message-ID: Hi, We'd like to report an issue we are facing with the COD's Optimade API. Using a SMILES string to search with COD website interface works fine: https://www.crystallography.net/cod/search.php SMILES: c1ccccc1 However, when the same SMILES value is used to query through Optimade API, we get no results back (and no errors either). Here is how we are searching with Optimade: https://www.crystallography.net/cod/optimade/structures?filter=_cod_smiles=%22c1ccccc1%22 Please let me know if you need any further information. Kind Regards, Mehmet. -- 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 grazulis at ibt.lt Fri May 23 13:55:49 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Fri, 23 May 2025 13:55:49 +0300 Subject: [Cod-bugs] Optimade API returns empty results for SMILES query, while web interface works properly for the same SMILES value In-Reply-To: References: Message-ID: Hi, Mehmet, thanks for the notification! We'll investigate the problem and come back to you. Regards, Saulius On 2025-05-23 13:51, Mehmet Giritli - STFC UKRI wrote: > Hi, > > We'd like to report an issue we are facing with the COD's Optimade API. > > Using a SMILES string to search with COD website interface works fine: > > https://www.crystallography.net/cod/search.php > SMILES: c1ccccc1 > > However, when the same SMILES value is used to query through Optimade > API, we get no results back (and no errors either). Here is how we are > searching with Optimade: > > https://www.crystallography.net/cod/optimade/structures?filter=_cod_smiles=%22c1ccccc1%22 > > Please let me know if you need any further information. > > Kind Regards, > Mehmet. > > -- > 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 -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353 mobile: (+370-684)-49802, (+370-614)-36366 -- 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: grazulis.vcf Type: text/vcard Size: 4 bytes Desc: not available URL: From andrius.merkys at gmail.com Fri May 23 17:47:04 2025 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Fri, 23 May 2025 17:47:04 +0300 Subject: [Cod-bugs] Optimade API returns empty results for SMILES query, while web interface works properly for the same SMILES value In-Reply-To: References: Message-ID: <5222d193-79d1-40ad-ab9f-6fee47109a7f@gmail.com> Dear Mehmet, On 2025-05-23 13:51, Mehmet Giritli - STFC UKRI wrote: > We'd like to report an issue we are facing with the COD's Optimade API. > > Using a SMILES string to search with COD website interface works fine: > > https://www.crystallography.net/cod/search.php > > SMILES: c1ccccc1 > > However, when the same SMILES value is used to query through Optimade > API, we get no results back (and no errors either). Here is how we are > searching with Optimade: > > https://www.crystallography.net/cod/optimade/structures?filter=_cod_smiles=%22c1ccccc1%22 > > Please let me know if you need any further information. You are right to observe that search by SMILES does not work in the current COD OPTIMADE interface. It is not implemented yet, and as such it should return an error. We will either implement the search or emit a proper error message in the next COD website update. Please mind that, when implemented, search by SMILES in COD OPTIMADE interface will not perform substructure search as is done in regular search interface. Most likely this will be string comparison instead, due to the complexity of substructure search. Best wishes, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, 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. From mehmet.giritli at stfc.ac.uk Fri May 23 17:54:32 2025 From: mehmet.giritli at stfc.ac.uk (Mehmet Giritli - STFC UKRI) Date: Fri, 23 May 2025 14:54:32 +0000 Subject: [Cod-bugs] Optimade API returns empty results for SMILES query, while web interface works properly for the same SMILES value In-Reply-To: <5222d193-79d1-40ad-ab9f-6fee47109a7f@gmail.com> References: <5222d193-79d1-40ad-ab9f-6fee47109a7f@gmail.com> Message-ID: Thank you Andrius. Best, Mehmet. ________________________________ From: Andrius Merkys Sent: 23 May 2025 15:47 To: Giritli, Mehmet (STFC,RAL,SC) Cc: Aileen Day ; Poulter, Gemma (STFC,RAL,SC) ; cod-bugs at ibt.lt Subject: Re: [Cod-bugs] Optimade API returns empty results for SMILES query, while web interface works properly for the same SMILES value Dear Mehmet, On 2025-05-23 13:51, Mehmet Giritli - STFC UKRI wrote: > We'd like to report an issue we are facing with the COD's Optimade API. > > Using a SMILES string to search with COD website interface works fine: > > https://www.crystallography.net/cod/search.php > > SMILES: c1ccccc1 > > However, when the same SMILES value is used to query through Optimade > API, we get no results back (and no errors either). Here is how we are > searching with Optimade: > > https://www.crystallography.net/cod/optimade/structures?filter=_cod_smiles=%22c1ccccc1%22 > > Please let me know if you need any further information. You are right to observe that search by SMILES does not work in the current COD OPTIMADE interface. It is not implemented yet, and as such it should return an error. We will either implement the search or emit a proper error message in the next COD website update. Please mind that, when implemented, search by SMILES in COD OPTIMADE interface will not perform substructure search as is done in regular search interface. Most likely this will be string comparison instead, due to the complexity of substructure search. Best wishes, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, 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: