From qiming.jia.24 at ucl.ac.uk Thu May 29 16:25:14 2025 From: qiming.jia.24 at ucl.ac.uk (Jia, Qiming) Date: Thu, 29 May 2025 13:25:14 +0000 Subject: [Cod-bugs] Programmatic Access to COD Data for Acentric Structures Message-ID: Dear COD Team, I?m a research student currently working on a project that requires downloading and processing crystallographic data from the COD, specifically focusing on non-centrosymmetric (acentric) structures for machine learning purposes. While trying to automate the search using search.php, I encountered difficulties?my script expected JSON responses, but it seems this endpoint is not designed for API use. I?ve explored the documentation but couldn?t find a confirmed method to programmatically filter or retrieve structures based on space groups or symmetry properties. Could you please advise if there is an officially supported way to access COD data programmatically for such purposes? Alternatively, is there a mirror or index file that you recommend for offline filtering of CIF files? Any guidance or sample script would be greatly appreciated. Best regards, Jason -- 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 toshiyuki.sasaki at spring8.or.jp Sat May 31 09:30:16 2025 From: toshiyuki.sasaki at spring8.or.jp (Toshiyuki Sasaki) Date: Sat, 31 May 2025 15:30:16 +0900 Subject: [Cod-bugs] COD Data registration In-Reply-To: References: <010a01db6e2c$26024160$7206c420$@spring8.or.jp> Message-ID: <02f501dbd1f5$78db6b00$6a924100$@spring8.or.jp> Dear Dr. Saulius Gra?ulis, I hope this email finds you well. I have just uploaded two new structures: 3000601 and 3000602. Regarding structure 3000602, please note that the line _refine_ls_wR_factor_ref 0.4244 was removed prior to deposition. Additionally, I have input the XRD information (XRD-00385) for both structures. I hope everything is in order with this submission. Sincerely yours, Toshiyuki Sasaki ************************************************************** ?????????????????? (Japan Synchrotron Radiation Research Institute (JASRI)) ???????? (Diffraction and Scattering Division) ??????????? (Tenure-track researcher) ?????? (Dr. Toshiyuki Sasaki) TEL: 050-3502-3649 (63430) ?679-5198????????????1??1?1? (1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 Japan) ************************************************************** From: Saulius Gra?ulis [mailto:grazulis at ibt.lt] Sent: Monday, April 28, 2025 6:01 PM To: Toshiyuki Sasaki Cc: cod-bugs at lists.crystallography.net Subject: Re: COD Data registration Dear Dr. Sasaki, than you once more for your depositions and for the thorough information, and my apologies that it took so long to respond. Your very interesting structures and comprehensive documentation in XRDa prompted us tu update the Crystallography Open Database and to include links to the original Raw Diffraction Data. With your three records, we start officially accepting links to the Raw Data Depositions :). Please have a look if the records we inserted are as you intended: https://www.crystallography.net/cod/3000559.html https://www.crystallography.net/cod/3000560.html https://www.crystallography.net/cod/3000561.html https://www.crystallography.net/cod/3000562.html Sincerely yours, Saulius PS. With our new COD database, you can insert the XRDa links into your new depositions like this: loop_ _cod_related_entry_id _cod_related_entry_database _cod_related_entry_code _cod_related_entry_description 1 XRDa 00999 DOI:10.51093/xrd-00999 where '00999' should be replaced by the actual identifier assigned by XRDa. With these lines the links to XRDa will be added automatically. PPS. Meanwhile, we will go through your other records, starting with COD 3000450, and will insert XRDa links and other information when needed. I will send you the links to these files after the updates. S.G. On 2025-01-24 08:49, Toshiyuki Sasaki wrote: Dear Dr. Saulius Gra?ulis, The deposited CIF files (COD accession codes: 3000559?3000562) were just released into publicly accessible repositories as published data by adding publication information. Published paper Chem. Eur. J. 2025, 31, e202403427 DOI: 10.1002/chem.202403427 Link: https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/chem.202403427 Here are DOI of XRDa (Xtal Raw Data Archive) and CCDC number: 3000559 XRDa DOI: 10.51093/xrd-00269 Link: https://xrda.pdbj.org/entry/269 CCDC: 2376461 3000560 XRDa DOI: 10.51093/xrd-00264 Link: https://xrda.pdbj.org/entry/264 CCDC: 2376462 3000561 XRDa DOI: 10.51093/xrd-00265 Link: https://xrda.pdbj.org/entry/265 CCDC: 2376463 3000562 XRDa: Not registered CCDC: 2376598 Sincerely yours, Toshiyuki Sasaki ************************************************************** ?????????????????? (Japan Synchrotron Radiation Research Institute (JASRI)) ???????? (Diffraction and Scattering Division) ??????????? (Tenure-track researcher) ?????? (Dr. Toshiyuki Sasaki) TEL: 050-3502-3649 (63430) ?679-5198????????????1??1?1? (1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 Japan) ************************************************************** -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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: