From martin.maly at mrc-lmb.cam.ac.uk Mon Sep 8 17:21:57 2025 From: martin.maly at mrc-lmb.cam.ac.uk (=?UTF-8?Q?Martin_Mal=C3=BD_-_MRC_LMB?=) Date: Mon, 8 Sep 2025 15:21:57 +0100 Subject: [Cod-bugs] Publication for 8106023 Message-ID: <1176940a-916c-4ecd-bc65-998203be167f@mrc-lmb.cam.ac.uk> Dear Sir or Madam, I think that this COD entry has incorrect metadata about its publication. Could you please check it and possibly correct? https://www.crystallography.net/cod/8106023.html Thank you. Best regards, Martin -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From andrius.merkys at gmail.com Tue Sep 9 13:24:59 2025 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Tue, 9 Sep 2025 13:24:59 +0300 Subject: [Cod-bugs] Publication for 8106023 In-Reply-To: <1176940a-916c-4ecd-bc65-998203be167f@mrc-lmb.cam.ac.uk> References: <1176940a-916c-4ecd-bc65-998203be167f@mrc-lmb.cam.ac.uk> Message-ID: <2cd8b913-38d8-4e41-bf65-6e6a57ab0c33@gmail.com> Dear Martin, On 2025-09-08 17:21, Martin Mal? - MRC LMB wrote: > I think that this COD entry has incorrect metadata about its > publication. Could you please check it and possibly correct? > > https://www.crystallography.net/cod/8106023.html Thanks for reporting this issue. I confirm that this COD entry contains the same crystal description as present in the supplementary material of the journal article it links to [1]. Interestingly, however, the article talks about a different chemical compound and a different crystal. To me it seems that there has been a mixup upstream, most likely by the authors. It would be best to write them and ask about the mismatch of the crystals. Best wishes, Andrius [1] https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2019-0514/html -- 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 bcao686 at connect.hkust-gz.edu.cn Wed Sep 10 08:33:53 2025 From: bcao686 at connect.hkust-gz.edu.cn (Bin CAO) Date: Wed, 10 Sep 2025 05:33:53 +0000 Subject: [Cod-bugs] Assistance with Uploading CIF File Message-ID: Dear COD Website Maintainer, I am Bin Cao, a researcher from HKUST Guangzhou. I encountered an issue while depositing a crystal structure in CIF format. Although the structure passes all tests successfully, the upload always fails. Could you please help me resolve this issue? Best regards, Bin Cao -- 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 Wed Sep 10 08:46:40 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Wed, 10 Sep 2025 08:46:40 +0300 Subject: [Cod-bugs] Assistance with Uploading CIF File In-Reply-To: References: Message-ID: Dear Bin Cao, thank you for the problem report. On 2025-09-10 08:33, Bin CAO wrote: > Dear COD Website Maintainer, > I am Bin Cao, a researcher from HKUST Guangzhou. I encountered an > issue while depositing a crystal structure in CIF format. Although the > structure passes all tests successfully, the upload always fails. We have currently been "attacked" by indiscriminate downloads from bots that overloaded the COD systems, and this left our deposition system in a crippled state. I have now unblocked the system ? could you please check if the deposition works now? If it still does not work, could you please send us a screenshot with the message hat you get, and/or the original CIF and the deposition session URL? I apologise for the inconveniences this causes. Sincerely yours, Saulius > Could you please help me resolve this issue? > Best regards, > Bin Cao > > > -- > 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) 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: From bcao686 at connect.hkust-gz.edu.cn Wed Sep 10 08:52:46 2025 From: bcao686 at connect.hkust-gz.edu.cn (Bin CAO) Date: Wed, 10 Sep 2025 05:52:46 +0000 Subject: [Cod-bugs] Assistance with Uploading CIF File In-Reply-To: References: Message-ID: Solved. Best regard, Bin Cao From: Saulius Gra?ulis Date: Wednesday, September 10, 2025 at 13:47 To: Bin CAO , cod-bugs at ibt.lt Subject: Re: [Cod-bugs] Assistance with Uploading CIF File You don't often get email from grazulis at ibt.lt. Learn why this is important Dear Bin Cao, thank you for the problem report. On 2025-09-10 08:33, Bin CAO wrote: Dear COD Website Maintainer, I am Bin Cao, a researcher from HKUST Guangzhou. I encountered an issue while depositing a crystal structure in CIF format. Although the structure passes all tests successfully, the upload always fails. We have currently been "attacked" by indiscriminate downloads from bots that overloaded the COD systems, and this left our deposition system in a crippled state. I have now unblocked the system ? could you please check if the deposition works now? If it still does not work, could you please send us a screenshot with the message hat you get, and/or the original CIF and the deposition session URL? I apologise for the inconveniences this causes. Sincerely yours, Saulius Could you please help me resolve this issue? Best regards, Bin Cao -- 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) 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. -- 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 husakm at vscht.cz Wed Sep 10 11:44:23 2025 From: husakm at vscht.cz (=?UTF-8?B?TWljaGFsIEh1xaHDoWs=?=) Date: Wed, 10 Sep 2025 10:44:23 +0200 Subject: [Cod-bugs] theoretical calculation results in COD Message-ID: Hi I was asked somebody during ECM35 conference to store our theoretically recalculated structures in COD .... Can I have related questions: 1) I see you have suggested a CIF DFT dictionary: https://wiki.crystallography.net/cif/dictionaries/ddl1/cif_dft/ Can I have some sample CIF files using this dictionary to be sure I understand the fields ? Results from CASTEP, Quantum Espresso are preferable (CP2K, CRYSTAL , VASP results are OK as well). It will be nice to see the output form the QM program and the CIF to validate the data correspondence ... 2) Can i search in COD only for calculated structures? (and e.g. specify some of the DFT fields) ? 3) How can I deposit recalculated structures (corresponding to some CSD or COD structures) ? Will they do not mix with experimental structures ? Michal Husak UCT Prague -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From grazulis at ibt.lt Thu Sep 11 14:49:15 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Thu, 11 Sep 2025 14:49:15 +0300 Subject: [Cod-bugs] theoretical calculation results in COD In-Reply-To: References: Message-ID: Dear Michal, thank you very much for your e-mail and for the offer of structure depositions! On 2025-09-10 11:44, Michal Hu??k wrote: > Hi > > I was asked somebody during ECM35 conference to store our > theoretically recalculated structures in COD .... That was probably me :). In any case, you send your mail to the right address :) > > Can I have related questions: > > 1) I see you have suggested a CIF DFT dictionary: > > https://wiki.crystallography.net/cif/dictionaries/ddl1/cif_dft/ > > Can I have some sample CIF files using this dictionary to be sure I > understand the fields ? We have recently discussed the similar example with our colleagues, so I will share the same example with you: > On 2025-06-18 12:09, Andrius Merkys wrote: > Below I list TCOD IDs (or their ranges) which originate from VASP: > > * 20000173: mentions VASP usage > > * range 20000419 -- 20000423: from VASP, has bulk modulus > > * range 20001806 -- 20002020: a bunch of structures from > doi:10.1103/physrevb.92.014106 converted from POSCAR format, has > POSCAR embedded in CIF > > * 20006288 and 20006289: seemingly from VASP, but contains no > calculation descriptions, just the coordinates. > > Most of them were manually curated (by me). 10 years ago I wrote a > (lossy) tool converting VASP XML to CIF with TCOD data items [1], but > I am not sure how well did it age - I have not used it for a while. I > could in principle revive it if there was any interest. The 8-digit IDs are IDs from the TCOD [1]. You can access structures over the Web from our server using the standard resolving URLs, e.g.: https://www.crystallography.net/tcod/20000173.html https://www.crystallography.net/tcod/20000173.cif Likewise for other examples: https://www.crystallography.net/tcod/20001806.html https://www.crystallography.net/tcod/20001806.cif You can also check out the full TCOD on your disk. The data are in a public Subversion repository; you can check it our ? on Linux the command will be: svn co svn://www.crystallography.net/tcod NB: we were recently "attacked" by Web bots that would indiscriminately download multiple CIFs, send tens of requests at once from different locations and download all historical CIFs (old revisions), which caused our servers to crash from overload. We there fore had to resort to limiting downloads to 20-30 CIFs per day and to block IP numbers that download much more. If you need more data, the better way (both for you and for us) is to get the whole TCOD using the "svn co" method :). If, however, you IP gets blocked for some reason, please e-mail me with your IP and we will whitelist it. The same applies to COD data :) > > Results from CASTEP, Quantum Espresso are preferable (CP2K, CRYSTAL , > VASP results are OK as well). The examples are mostly from VASP; but I think we have QE examples as well. Please let me know if you are interested in these as well and you can not find them in the TCOD data. > > It will be nice to see the output form the QM program and the CIF to > validate the data correspondence ... Some files contain VASP and QE inputs. > > 2) Can i search in COD only for calculated structures? (and e.g. > specify some of the DFT fields) ? It has been decided that calculated structures should go to TCOD, and experimental (i.e. refined against diffraction or other measurement data) will be stored in the COD. It happens, however, that sometimes theoretical structures end up in the COD before we spot them (mostly from publication supplementary materials). If this happens, since COD ID is a stable identifier, we do not delete the COD structure but mark it in the database column `method` with the value "theoretical". In the CIFs themselves, the data are marked with the data item "_cod_struct_determination_method theoretical". To search for the theoretical structures, in the COD you have three methods: - check out the full COD CIF collection using "svn co svn://www.crystallography.net/cod/cif cod-cif" (caution: 190G checkout...) and then run something like this: find cod-cif/ -name '*.cif' | xargs grep -l "_cod_struct_determination_method? *theoretical" on the obtained files to get the list of identified theoretical ones, or - query the COD SQL directly: mysql -h sql.crystallography.net -u cod_reader cod -e 'select file from data where method = "theoretical"' - query structures on the Web and check the "include theoretical structures" box on the Web form; this will give yo both theoretical *and* experimental structures, but if you then search for only experimental structures and then subtract that set from the previous one, the remaining ones will be theoretical. In the TCOD, all structures are theoretical. > > 3) How can I deposit recalculated structures (corresponding to some > CSD or COD structures) ? Will they do not mix with experimental > structures ? Good point ? as said, in order to not mix theoretical and experimental structures, we should deposit theoretical structures to the TCOD [1]. There is a "deposit your data" link on the Web, and for larger sets we have programmatic deposition (please let us know if you would like to use it). The procedure for deposition is the same as for the COD database. HTH, Yours, Saulius > > Michal Husak > > UCT Prague > > > References: [1] Theoretical Crystallography Open Database (2025) https://www.crystallography.net/tcod -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) 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.