From toshiyuki.sasaki at spring8.or.jp Fri Aug 2 08:04:58 2024 From: toshiyuki.sasaki at spring8.or.jp (Toshiyuki Sasaki) Date: Fri, 2 Aug 2024 14:04:58 +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> Message-ID: <02c501dae499$85a9adf0$90fd09d0$@spring8.or.jp> 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From grazulis at ibt.lt Fri Aug 2 12:02:25 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Fri, 2 Aug 2024 12:02:25 +0300 Subject: [Cod-bugs] COD Data registration In-Reply-To: <02c501dae499$85a9adf0$90fd09d0$@spring8.or.jp> 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: 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: grazulis.vcf Type: text/vcard Size: 4 bytes Desc: not available URL: From grazulis at ibt.lt Sat Aug 3 13:49:14 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Sat, 3 Aug 2024 13:49:14 +0300 Subject: [Cod-bugs] AMCSD duplicate atoms and missing aniso links? Message-ID: <8e52e340-f530-666c-2a38-0a0d29e6b142@ibt.lt> Hi, Bob! How are you? I'm currently doing COD data validation, and I'm running into two issues that I would need your help to resolve. 1. Some AMCSD entries (e.g. COD ID 9015515 [1], AMCSD ID "0019710" [2]) have recently received the '_atom_site_aniso_[]' loop. This is great, but in some cases atom site labels in the _atom_site_[] loop do not match: > loop_ > _atom_site_aniso_label > _atom_site_aniso_U_11 > _atom_site_aniso_U_22 > _atom_site_aniso_U_33 > _atom_site_aniso_U_12 > _atom_site_aniso_U_13 > _atom_site_aniso_U_23 > # ... > *Pb'* 0.03159 0.03245 0.01811 0.01856 -0.00932 -0.00819 > # ... vs.: > loop_ > _atom_site_label > _atom_site_fract_x > _atom_site_fract_y > _atom_site_fract_z > _atom_site_occupancy > _atom_site_U_iso_or_equiv > # ... > *Pb** 0.10313 0.33075 0.34924 0.19800 0.02774 > # ... Can I assume that the atoms with quotes and atoms with stars are the same, e.g. that "Pb'" and "Pb*" is the same atom? I have written a script to fix this under the above-mentioned assumptions, and I'm about to commit the changes to the COD. It would be great to propagate these changes back to AMCSD, what you think? (Actually, I had the same issue with atom names containing hyphens, e.g. 'OH1' and 'O-H1', but I see that this issue is already fixed in AMCSD; I've updated the COD accordingly :). 2. In some places (56 COD entries) there are duplicate atom labels. When these are in two loops, we can not decide unambiguously which ANISO entry pertains to which atom. Example (from COD ID 9000543 [3], AMCSD ID "0000554"): > loop_ > _atom_site_aniso_label > _atom_site_aniso_U_11 > _atom_site_aniso_U_22 > _atom_site_aniso_U_33 > _atom_site_aniso_U_12 > _atom_site_aniso_U_13 > _atom_site_aniso_U_23 > # ... > *Mg* 0.00977 0.01092 0.00940 0.00000 0.00000 0.00000 > *Mg* 0.01490 0.00863 0.00956 0.00008 -0.00278 0.00053 > # ... and > loop_ > _atom_site_label > _atom_site_fract_x > _atom_site_fract_y > _atom_site_fract_z > _atom_site_occupancy > # ... > *Mg* 0.00720 0.39590 0.50000 0.21400 > *Mg* 0.25000 0.50000 0.25000 1.00000 > # ... Can I assume, in general, that the atoms in both loops in the same order, and number them 'Mg1' and 'Mg2' correspondingly? Like this: > loop_ > _atom_site_aniso_label > _atom_site_aniso_U_11 > _atom_site_aniso_U_22 > _atom_site_aniso_U_33 > _atom_site_aniso_U_12 > _atom_site_aniso_U_13 > _atom_site_aniso_U_23 > # ... > *Mg**1* 0.00977 0.01092 0.00940 0.00000 0.00000 0.00000 > *Mg**2* 0.01490 0.00863 0.00956 0.00008 -0.00278 0.00053 > # ... and > loop_ > _atom_site_label > _atom_site_fract_x > _atom_site_fract_y > _atom_site_fract_z > _atom_site_occupancy > # ... > *Mg**1* 0.00720 0.39590 0.50000 0.21400 > *Mg**2* 0.25000 0.50000 0.25000 1.00000 > # ... I would do this for the COD (probably manually). Again, it would be great to back-propagate these changes to the AMCSD collection. I can send you the lists of changed files or the list of problematic entries of the would help. Cheers, Saulius Refs.: [1] http://www.crystallography.net/cod/9015515.cif, http://www.crystallography.net/cod/9015515.html [2] https://rruff.geo.arizona.edu/AMS/CIF_text_files/05517_cif.txt [3] http://www.crystallography.net/cod/9000543.cif, http://www.crystallography.net/cod/9000543.html [4] https://rruff.geo.arizona.edu/AMS/CIF_text_files/00635_cif.txt -- 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 rdowns at arizona.edu Sat Aug 3 22:48:31 2024 From: rdowns at arizona.edu (Downs, Robert T - (rdowns)) Date: Sat, 3 Aug 2024 19:48:31 +0000 Subject: [Cod-bugs] [EXT] AMCSD duplicate atoms and missing aniso links? In-Reply-To: <8e52e340-f530-666c-2a38-0a0d29e6b142@ibt.lt> References: <8e52e340-f530-666c-2a38-0a0d29e6b142@ibt.lt> Message-ID: Saulius, I will replace every single quote ? in atom names in the entire database. You won?t see the changes until I rebuild it however, and that wont be for a month or so. Thanks for pointing in out to me. If you see any issues with double quotes ? let me know. Thanks, Bob From: Saulius Gra?ulis Sent: Saturday, August 3, 2024 3:49 AM To: Bob Downs Cc: cod-bugs at lists.crystallography.net; kicis at lists.crystallography.net Subject: [EXT] AMCSD duplicate atoms and missing aniso links? External Email ________________________________ Hi, Bob! How are you? I'm currently doing COD data validation, and I'm running into two issues that I would need your help to resolve. 1. Some AMCSD entries (e.g. COD ID 9015515 [1], AMCSD ID "0019710" [2]) have recently received the '_atom_site_aniso_[]' loop. This is great, but in some cases atom site labels in the _atom_site_[] loop do not match: loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 # ... Pb' 0.03159 0.03245 0.01811 0.01856 -0.00932 -0.00819 # ... vs.: loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy _atom_site_U_iso_or_equiv # ... Pb* 0.10313 0.33075 0.34924 0.19800 0.02774 # ... Can I assume that the atoms with quotes and atoms with stars are the same, e.g. that "Pb'" and "Pb*" is the same atom? I have written a script to fix this under the above-mentioned assumptions, and I'm about to commit the changes to the COD. It would be great to propagate these changes back to AMCSD, what you think? (Actually, I had the same issue with atom names containing hyphens, e.g. 'OH1' and 'O-H1', but I see that this issue is already fixed in AMCSD; I've updated the COD accordingly :). 2. In some places (56 COD entries) there are duplicate atom labels. When these are in two loops, we can not decide unambiguously which ANISO entry pertains to which atom. Example (from COD ID 9000543 [3], AMCSD ID "0000554"): loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 # ... Mg 0.00977 0.01092 0.00940 0.00000 0.00000 0.00000 Mg 0.01490 0.00863 0.00956 0.00008 -0.00278 0.00053 # ... and loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy # ... Mg 0.00720 0.39590 0.50000 0.21400 Mg 0.25000 0.50000 0.25000 1.00000 # ... Can I assume, in general, that the atoms in both loops in the same order, and number them 'Mg1' and 'Mg2' correspondingly? Like this: loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 # ... Mg1 0.00977 0.01092 0.00940 0.00000 0.00000 0.00000 Mg2 0.01490 0.00863 0.00956 0.00008 -0.00278 0.00053 # ... and loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy # ... Mg1 0.00720 0.39590 0.50000 0.21400 Mg2 0.25000 0.50000 0.25000 1.00000 # ... I would do this for the COD (probably manually). Again, it would be great to back-propagate these changes to the AMCSD collection. I can send you the lists of changed files or the list of problematic entries of the would help. Cheers, Saulius Refs.: [1] http://www.crystallography.net/cod/9015515.cif, http://www.crystallography.net/cod/9015515.html [2] https://rruff.geo.arizona.edu/AMS/CIF_text_files/05517_cif.txt [3] http://www.crystallography.net/cod/9000543.cif, http://www.crystallography.net/cod/9000543.html [4] https://rruff.geo.arizona.edu/AMS/CIF_text_files/00635_cif.txt -- 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: