From ohnishi.yusuke.corefc at osaka-u.ac.jp Mon Oct 6 14:53:30 2025 From: ohnishi.yusuke.corefc at osaka-u.ac.jp (ohnishi.yusuke.corefc at osaka-u.ac.jp) Date: Mon, 6 Oct 2025 11:53:30 +0000 Subject: [Cod-bugs] Micro-ED structures with high R_factors could not be deposited to COD as they are Message-ID: Dear COD support, I am Yusuke Ohnishi at the University of Osaka, Japan. We deposited 5 entries to COD (ID: 3000620~3000624). We had to comment out _refine_ls_R_factor_gt and _refine_ls_wR_factor_ref items; otherwise the Web interface did not accept the depositions. Could you please uncomment these lines on the server? They are MicroED structures refined only kinematically. Thus, traditional X-ray crystallography thresholds are not adequate. Best regards, Yusuke ????? (Ohnishi Yusuke) The University of Osaka Core Facility Center Specially Appointed Assistant Professor I-405, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan Tel: 06-6879-4815 Email: ohnishi.yusuke.corefc at osaka-u.ac.jp -- 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 andrius.merkys at gmail.com Mon Oct 6 15:14:12 2025 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Mon, 6 Oct 2025 15:14:12 +0300 Subject: [Cod-bugs] Micro-ED structures with high R_factors could not be deposited to COD as they are In-Reply-To: References: Message-ID: <580f6d0c-b710-4eed-94e7-f5ab6fcca895@gmail.com> Dear Yusuke, On 2025-10-06 14:53, ohnishi.yusuke.corefc at osaka-u.ac.jp wrote: > I am Yusuke Ohnishi at the University of Osaka, Japan. > > We deposited 5?entries to COD (ID: 3000620~3000624). > We had to comment out _refine_ls_R_factor_gt and > _refine_ls_wR_factor_ref items; otherwise the Web interface did not > accept the depositions. > Could you please uncomment these lines on the server? Could you please send me the values of _refine_ls_R_factor_gt and _refine_ls_wR_factor_ref data items of the aforementioned CIF depositions? I assume you have commented out these data items using '#' symbol as is usual in CIF syntax, however, our software filters out CIF comments. As a result, I cannot see these data items in the deposited files. > They are MicroED structures refined only kinematically. > Thus, traditional X-ray crystallography thresholds are not adequate. Thank you, we are aware of this, and are in the process of lowering the thresholds for MicroED structures. Best wishes, Andrius Merkys -- 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 ohnishi.yusuke.corefc at osaka-u.ac.jp Tue Oct 7 03:43:20 2025 From: ohnishi.yusuke.corefc at osaka-u.ac.jp (ohnishi.yusuke.corefc at osaka-u.ac.jp) Date: Tue, 7 Oct 2025 00:43:20 +0000 Subject: [Cod-bugs] Micro-ED structures with high R_factors could not be deposited to COD as they are In-Reply-To: <580f6d0c-b710-4eed-94e7-f5ab6fcca895@gmail.com> References: <580f6d0c-b710-4eed-94e7-f5ab6fcca895@gmail.com> Message-ID: Dear Andrius, I appreciate for your coorporation. Could you please send me the values of _refine_ls_R_factor_gt and _refine_ls_wR_factor_ref data items of the aforementioned CIF depositions? The values are below. ID 3000620 _refine_ls_R_factor_gt 0.1807 _refine_ls_wR_factor_ref 0.4132 ID 3000621 _refine_ls_R_factor_gt 0.1112 _refine_ls_wR_factor_ref 0.3086 ID 3000622 _refine_ls_R_factor_gt 0.1336 _refine_ls_wR_factor_ref 0.3493 ID 3000623 _refine_ls_R_factor_gt 0.1623 _refine_ls_wR_factor_ref 0.4271 ID 3000624 _refine_ls_R_factor_gt 0.1612 _refine_ls_wR_factor_ref 0.4132 Best regards, Yusuke ________________________________ ???: Andrius Merkys ????: 2025?10?6? 21:14 ??: ????? CC: ????? ; cod-bugs at ibt.lt ??: Re: [Cod-bugs] Micro-ED structures with high R_factors could not be deposited to COD as they are Dear Yusuke, On 2025-10-06 14:53, ohnishi.yusuke.corefc at osaka-u.ac.jp wrote: > I am Yusuke Ohnishi at the University of Osaka, Japan. > > We deposited 5 entries to COD (ID: 3000620~3000624). > We had to comment out _refine_ls_R_factor_gt and > _refine_ls_wR_factor_ref items; otherwise the Web interface did not > accept the depositions. > Could you please uncomment these lines on the server? Could you please send me the values of _refine_ls_R_factor_gt and _refine_ls_wR_factor_ref data items of the aforementioned CIF depositions? I assume you have commented out these data items using '#' symbol as is usual in CIF syntax, however, our software filters out CIF comments. As a result, I cannot see these data items in the deposited files. > They are MicroED structures refined only kinematically. > Thus, traditional X-ray crystallography thresholds are not adequate. Thank you, we are aware of this, and are in the process of lowering the thresholds for MicroED structures. Best wishes, Andrius Merkys -- 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: From grazulis at ibt.lt Tue Oct 7 09:23:59 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Tue, 7 Oct 2025 09:23:59 +0300 Subject: [Cod-bugs] Micro-ED structures with high R_factors could not be deposited to COD as they are In-Reply-To: References: Message-ID: Dear Yusuke, thank you for your e-mail and for the data deposition! On 2025-10-06 14:53, ohnishi.yusuke.corefc at osaka-u.ac.jp wrote: > We deposited 5?entries to COD (ID: 3000620~3000624). > We had to comment out _refine_ls_R_factor_gt and > _refine_ls_wR_factor_ref items; otherwise the Web interface did not > accept the depositions. > Could you please uncomment these lines on the server? OK, I'll insert back the T factor data. > > They are MicroED structures refined only kinematically. > Thus, traditional X-ray crystallography thresholds are not adequate. > Fair enough. This looks like an important comment on your deposited structure. Is it OK if I insert these two sentences as "depositor comments" on your behalf? 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: