From toshiyuki.sasaki at spring8.or.jp Tue Sep 17 04:38:42 2024 From: toshiyuki.sasaki at spring8.or.jp (Toshiyuki Sasaki) Date: Tue, 17 Sep 2024 10:38:42 +0900 Subject: [Cod-bugs] COD Data registration In-Reply-To: References: <006701d9ae4b$cc8d8ff0$65a8afd0$@spring8.or.jp> <7179b502-51ad-38ad-ba82-62e192d93919@ibt.lt> <026c01d9b0ab$d9170140$8b4503c0$@spring8.or.jp> <004501da436b$db9a11c0$92ce3540$@spring8.or.jp> <002701da4420$21774dc0$6465e940$@spring8.or.jp> <21e3544a-9e79-490e-94e5-2fe824a15ed5@ibt.lt> <007701dac859$4cc081a0$e64184e0$@spring8.or.jp> <02c501dae499$85a9adf0$90fd09d0$@spring8.or.jp> Message-ID: <004201db08a2$5447fe10$fcd7fa30$@spring8.or.jp> Dear Dr. Saulius Gra?ulis, The deposited CIF files (COD accession codes: 3000469?3000476) were just released into publicly accessible repositories as published data by adding publication information. Published paper Cryst. Growth Des. 2024, 24, 17, 7222?7234 DOI: 10.1021/acs.cgd.4c00856 Link: https://pubs.acs.org/doi/10.1021/acs.cgd.4c00856 Here are DOI of XRDa (Xtal Raw Data Archive): 3000470 DOI: 10.51093/xrd-00261 Link: https://xrda.pdbj.org/entry/261 3000472 DOI: 10.51093/xrd-00262 Link: https://xrda.pdbj.org/entry/262 3000474 DOI: 10.51093/xrd-00263 Link: https://xrda.pdbj.org/entry/263 3000476 DOI: 10.51093/xrd-00217 Link: https://xrda.pdbj.org/entry/217 Sincerely yours, Toshiyuki Sasaki ************************************************************** ?????????????????? (Japan Synchrotron Radiation Research Institute (JASRI)) ???????? (Diffraction and Scattering Division) ??????????? (Tenure-track researcher) ?????? (Dr. Toshiyuki Sasaki) TEL: 0791-58-0802(3430) ?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: Friday, August 2, 2024 6:02 PM To: Toshiyuki Sasaki Cc: cod-bugs at lists.crystallography.net Subject: Re: COD Data registration Dear Dr. Toshiyuki, thank you for the e-mail! I'll insert the ...R_factor_... data names into you submitted CIFs where necessary. Regarding the references to the image locations, there are two mechanisms that that we consider using. One is the IUCr suggestion by Brian McMahon announced at the IUCr Congress last year. Another is the intrinsic COD mechanism using the '_cod_related_entry_[]' category. Both requite certain update of the COD infrastructure, which I plan to do, hopefully, before leaving to the ECM34 this month. The '_cod_related_entry_[]' at the moment looks like this: saulius at tasmanijos-velnias cod-tools/ $ tail -5 /home/saulius/struct/cod/current/cif/9/01/51/9015157.cif loop_ _cod_related_entry_id _cod_related_entry_database _cod_related_entry_code 1 AMCSD 0018609 In a similar way, we could use an external database, say XRDA [1], and gibe a link to the database's record (unique ID). For this I need to make an additional SQL table in the COD, xrda_x_cod, and update the COD deposition scripts so that they populate that new table. It is not a large work, I just need to find two free days to implement and test this :) BTW, will your your colleagues be at the ECM34? It would be nice to meet and talk in person :) Regards, Saulius On 2024-08-02 08:04, Toshiyuki Sasaki wrote: Dear Dr. Saulius Gra?ulis, I have uploaded crystal structures with some errors solved by MicroED to COD. By following the previous procedures (remove lines and give you information about the errors etc.), I would like you to handle the data properly. Deposited data and related information 3000560: merged 13 crystals Removed lines for the deposition _refine_ls_wR_factor_ref 0.4090 3000561: merged 9 crystals Removed lines for the deposition _refine_ls_R_factor_gt 0.1540 _refine_ls_wR_factor_ref 0.3972 Regarding EM images, what can I do? ?I'll come back to your shortly with a suggested update of your data files.? Thank you for your cooperation. Best regards, Toshiyuki ************************************************************** ?????????????????? (Japan Synchrotron Radiation Research Institute (JASRI)) ???????? (Diffraction and Scattering Division) ??????????? (Tenure-track researcher) ?????? (Dr. Toshiyuki Sasaki) TEL: 0791-58-0802(3430) ?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: Thursday, June 27, 2024 3:18 PM To: Toshiyuki Sasaki Cc: cod-bugs at lists.crystallography.net Subject: Re: COD Data registration On 2024-06-27 09:14, Toshiyuki Sasaki wrote: Finally our paper was published on Journal of Materials Chemistry C. The deposited CIF files (3000450, 3000451) were just updated by including publication information. In addition, I give you DOI of XRDa of these structures as I promised. 3000450, 3000451: 10.51093/xrd-00142 Thanks a lot for your update, and congratulations with your publication! I'll have a look at the data. Also, I remember that your have published the links to original EM images; it would be great to include these links into the COD files as well. We have recently developed a mechanism how this can be done,; I'll come back to your shortly with a suggested update of your data files. Sincerely yours, Saulius -- 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. -- 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: