From grazulis at ibt.lt Mon Jan 6 22:04:55 2020 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Mon, 6 Jan 2020 22:04:55 +0200 Subject: [Cod-bugs] COD conversion with HighScore In-Reply-To: References: Message-ID: Dear Thomas & Thomas, On 2020-01-03 22:00, Thomas Degen wrote: > We are indeed processing "_atom_site_type_symbol", but this > information is missing for many COD entries. It would be great if the > chemical element (type symbol) would be unambiguously supplied for > each Atom, we would very much appreciate this. I have made a survey of structures that have "uncanonical" atom names (the data list files, *.lst, and logs with Unix commands that were used to generate them are on my server: http://saulius-grazulis.lt/~saulius/COD-uncanonical-atoms/). There are 8360 structures currently in the COD with atom names that do not match the periodic table (wc -l COD-structure-with-uncanonical-atoms-counts.lst). This seems doable with an automatic script. The most frequent "strange" atom names are: > saulius at varanas COD-uncanonical-atoms/ $ head -n 21 COD-uncanonical-atom-counts.lst | grep -v '\?' > 5018 h > 4653 c > 4264 Wat > 2775 MgM > 2341 FeM > 2169 SiT > 2103 AlT > 1602 AlM > 1515 n > 1095 MnM > 828 TiM > 825 CaM > 758 MgT > 686 CL > 649 NaA > 555 o > 550 FeT > 539 NaM > 520 OW > 455 KA The Wat is most probably water, and we can fix that. We'll have to guess that 'h' is hydrogen, 'c' is carbon and 'CL' is chlorine. If we make such guess, we can check only selected structures to see if this is so. AlM is probably Aluminium, and other metals are also marked with site M sign ? we can correct this. More tricky examples are rare: "SIII" might be "Si II" (the second silicon), or "S III" (the third sulphur). But there are only two of these in the whole COD, so we can check them by hand. For all these atoms we would add _atom_site_type_symbol, and, if the existing _atom_site_type_symbol is converted to different case, we will fix the _atom_type_symbol accordingly. The most tricky part is 'NaAm', 'BiMe' or 'CuZn'. Some are single metal on different sites; we can figure out which are which by comparing coordinates and occupancies. Bu the CuZn site seems to be mixed Cu and Zn atom site, and no relative occupancies are given ? so we can not resolve them. We'll have to leave this particular CIF as it is (unless we can find more data in the paper). Would such fixes be helpful to you, Thomas? If yes, we think about how to implement them. The bes would be to get a good student to do it as a practicum (under the COD team supervision :). Regards, Saulius -- 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. From thomas.degen at panalytical.com Mon Jan 6 22:37:44 2020 From: thomas.degen at panalytical.com (Thomas Degen) Date: Mon, 6 Jan 2020 20:37:44 +0000 Subject: [Cod-bugs] {Spam?} RE: COD conversion with HighScore In-Reply-To: References: Message-ID: Dear Saulius, Sorry for not replying yet on your last email but I was swamped by other work today. Wow, that information is already very helpful, we can use this to improve our conversion by looking for some of these cases and apply appropriate fixes Let me answer later in more detail I need to talk to colleagues first. Thanks and best regards, Thomas -----Original Message----- From: Saulius Gra?ulis Sent: Monday, January 6, 2020 9:05 PM To: Thomas Degen ; Thomas Dortmann ; cod-bugs at ibt.lt Cc: Thomas Dortmann Subject: Re: [Cod-bugs] COD conversion with HighScore Dear Thomas & Thomas, On 2020-01-03 22:00, Thomas Degen wrote: > We are indeed processing "_atom_site_type_symbol", but this > information is missing for many COD entries. It would be great if the > chemical element (type symbol) would be unambiguously supplied for > each Atom, we would very much appreciate this. I have made a survey of structures that have "uncanonical" atom names (the data list files, *.lst, and logs with Unix commands that were used to generate them are on my server: https://eur01.safelinks.protection.outlook.com/?url=http:%2F%2Fsaulius-grazulis.lt%2F~saulius%2FCOD-uncanonical-atoms%2F&data=01%7C01%7Cthomas.degen%40panalytical.com%7Cd6cdd3ad3d3648b9ba2608d792e3b65a%7C071061f3d56946889edeb63a6a7f1ecc%7C0&sdata=3HVhmHnoMQwUwNS9gcLAujSb60pU%2BxzlrAxXfUlxCY8%3D&reserved=0). There are 8360 structures currently in the COD with atom names that do not match the periodic table (wc -l COD-structure-with-uncanonical-atoms-counts.lst). This seems doable with an automatic script. The most frequent "strange" atom names are: > saulius at varanas COD-uncanonical-atoms/ $ head -n 21 COD-uncanonical-atom-counts.lst | grep -v '\?' > 5018 h > 4653 c > 4264 Wat > 2775 MgM > 2341 FeM > 2169 SiT > 2103 AlT > 1602 AlM > 1515 n > 1095 MnM > 828 TiM > 825 CaM > 758 MgT > 686 CL > 649 NaA > 555 o > 550 FeT > 539 NaM > 520 OW > 455 KA The Wat is most probably water, and we can fix that. We'll have to guess that 'h' is hydrogen, 'c' is carbon and 'CL' is chlorine. If we make such guess, we can check only selected structures to see if this is so. AlM is probably Aluminium, and other metals are also marked with site M sign ? we can correct this. More tricky examples are rare: "SIII" might be "Si II" (the second silicon), or "S III" (the third sulphur). But there are only two of these in the whole COD, so we can check them by hand. For all these atoms we would add _atom_site_type_symbol, and, if the existing _atom_site_type_symbol is converted to different case, we will fix the _atom_type_symbol accordingly. The most tricky part is 'NaAm', 'BiMe' or 'CuZn'. Some are single metal on different sites; we can figure out which are which by comparing coordinates and occupancies. Bu the CuZn site seems to be mixed Cu and Zn atom site, and no relative occupancies are given ? so we can not resolve them. We'll have to leave this particular CIF as it is (unless we can find more data in the paper). Would such fixes be helpful to you, Thomas? If yes, we think about how to implement them. The bes would be to get a good student to do it as a practicum (under the COD team supervision :). Regards, Saulius -- 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. This email and any files transmitted with it are confidential and maybe legally privileged. Such message is intended solely for the use of the individual or entity to whom they are addressed. Please notify the originator of the message if you are not the intended recipient and destroy all copies of the message. Please note that any use, dissemination, or reproduction is strictly prohibited and may be unlawful. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From ams at AdvancedMolecularSciences.com Tue Jan 7 01:27:22 2020 From: ams at AdvancedMolecularSciences.com (Abelardo M. Silva) Date: Mon, 6 Jan 2020 18:27:22 -0500 Subject: [Cod-bugs] Question about COD Message-ID: An HTML attachment was scrubbed... URL: From thomas.dortmann at panalytical.com Wed Jan 8 18:22:49 2020 From: thomas.dortmann at panalytical.com (Thomas Dortmann) Date: Wed, 8 Jan 2020 16:22:49 +0000 Subject: [Cod-bugs] COD conversion with HighScore In-Reply-To: References: Message-ID: Hi Saulius! Thanks a lot for your letters and explanations. I'm sorry that it took a while to discuss your input and write this answer. One problem is the CIF syntax, which allows for a lot of freedom (= better readability), but must not be unique, when interpreted by software. Unfortunately this will not change, and for sure not for already existing CIFs. Converting the CIFs from the COD (to generate peak lists and profiles for search-match), we experience the following problems: 1. atom_names are not translated correctly into atom_symbols: We already correct most from your list of 33900 entries, only the "Wat" name was missing and got translated into "At". This is fixed now, but we would really prefer to find correct atom_symbols in all CIFs. Still there is a number of CIFs where the atom_names are not interpreted: 1235 warnings (Btw.: "n" could be either nitrogen or a multiplier, we are not sure) 2. Anisotropic displacement parameters are way too big; often isotropic values don't match anisotropic values in these cases: We convert from Us or Betas to Bs; the warning identifies one or more Bansio values >= 10. This results in wrong phase quantitations with the Rietveld method. (We also recalculate Biso from the Banisos, when Biso is missing) This is the biggest group of CIFs generating warnings during the conversion: 123.717 warnings 3. invalid space group: 454 CIFs You find a list of all CIFs throwing warnings during conversion in the attached Excel sheet, ordered by the type of warning and the COD ID number. I hope this will help to correct errors in the COD and to make it better applicable through time. Please let me know when you need more information, or want additional checks during our conversions to find out more details. Discussing things with my boss it looks like we are not going to put real effort (like paying a student) into this, because this would help the competition as well. best regards, Thomas Dortmann -----Original Message----- From: Saulius Gra?ulis Sent: 06 January 2020 21:05 To: Thomas Degen ; Thomas Dortmann ; cod-bugs at ibt.lt Cc: Thomas Dortmann Subject: Re: [Cod-bugs] COD conversion with HighScore Dear Thomas & Thomas, On 2020-01-03 22:00, Thomas Degen wrote: > We are indeed processing "_atom_site_type_symbol", but this > information is missing for many COD entries. It would be great if the > chemical element (type symbol) would be unambiguously supplied for > each Atom, we would very much appreciate this. I have made a survey of structures that have "uncanonical" atom names (the data list files, *.lst, and logs with Unix commands that were used to generate them are on my server: https://eur01.safelinks.protection.outlook.com/?url=http:%2F%2Fsaulius-grazulis.lt%2F~saulius%2FCOD-uncanonical-atoms%2F&data=01%7C01%7Cthomas.dortmann%40panalytical.com%7Cd6cdd3ad3d3648b9ba2608d792e3b65a%7C071061f3d56946889edeb63a6a7f1ecc%7C0&sdata=QQ95rzT24YIl3o0PI15XYegtPFQvUUGmOC9fwve%2B3Mw%3D&reserved=0). There are 8360 structures currently in the COD with atom names that do not match the periodic table (wc -l COD-structure-with-uncanonical-atoms-counts.lst). This seems doable with an automatic script. The most frequent "strange" atom names are: > saulius at varanas COD-uncanonical-atoms/ $ head -n 21 COD-uncanonical-atom-counts.lst | grep -v '\?' > 5018 h > 4653 c > 4264 Wat > 2775 MgM > 2341 FeM > 2169 SiT > 2103 AlT > 1602 AlM > 1515 n > 1095 MnM > 828 TiM > 825 CaM > 758 MgT > 686 CL > 649 NaA > 555 o > 550 FeT > 539 NaM > 520 OW > 455 KA The Wat is most probably water, and we can fix that. We'll have to guess that 'h' is hydrogen, 'c' is carbon and 'CL' is chlorine. If we make such guess, we can check only selected structures to see if this is so. AlM is probably Aluminium, and other metals are also marked with site M sign ? we can correct this. More tricky examples are rare: "SIII" might be "Si II" (the second silicon), or "S III" (the third sulphur). But there are only two of these in the whole COD, so we can check them by hand. For all these atoms we would add _atom_site_type_symbol, and, if the existing _atom_site_type_symbol is converted to different case, we will fix the _atom_type_symbol accordingly. The most tricky part is 'NaAm', 'BiMe' or 'CuZn'. Some are single metal on different sites; we can figure out which are which by comparing coordinates and occupancies. Bu the CuZn site seems to be mixed Cu and Zn atom site, and no relative occupancies are given ? so we can not resolve them. We'll have to leave this particular CIF as it is (unless we can find more data in the paper). Would such fixes be helpful to you, Thomas? If yes, we think about how to implement them. The bes would be to get a good student to do it as a practicum (under the COD team supervision :). Regards, Saulius -- 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. This email and any files transmitted with it are confidential and maybe legally privileged. Such message is intended solely for the use of the individual or entity to whom they are addressed. Please notify the originator of the message if you are not the intended recipient and destroy all copies of the message. Please note that any use, dissemination, or reproduction is strictly prohibited and may be unlawful. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- A non-text attachment was scrubbed... Name: COD_Conv_Warnings.xlsx Type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet Size: 3940157 bytes Desc: COD_Conv_Warnings.xlsx URL: From ontaii at 163.com Thu Jan 9 13:40:07 2020 From: ontaii at 163.com (Wen Dawei) Date: Thu, 9 Jan 2020 19:40:07 +0800 (CST) Subject: [Cod-bugs] Problem: fail to search anything Message-ID: <3ae58c9d.8e21.16f8a1ac44a.Coremail.ontaii@163.com> Hello, I have been using COD for years and I feel grateful for the works. Recently, I found a problem when I tried to search some crystal structure in COD. For example, when I tried to search "NaCl" (or something like "Al2O3"), but the system told me "there are no files matching your search criteria". That's strange. I have never met such problem before. Is there anything with my input or there are bugs in recent version of COD? (For the conditions, please see the appendix files. I failed no matter I filled the "number of distinct elements min and max" or not.) Best regards. -- Jiangmen, Guangdong, 529020, China Wuyi University School of Applied Physics and Materials Dawei Wen ???????? ???? ????????? ??? -- 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: condition.png Type: image/png Size: 53845 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: result.png Type: image/png Size: 54104 bytes Desc: not available URL: From merkys at ibt.lt Thu Jan 9 13:52:59 2020 From: merkys at ibt.lt (Andrius Merkys) Date: Thu, 9 Jan 2020 13:52:59 +0200 Subject: [Cod-bugs] Problem: fail to search anything In-Reply-To: <3ae58c9d.8e21.16f8a1ac44a.Coremail.ontaii@163.com> References: <3ae58c9d.8e21.16f8a1ac44a.Coremail.ontaii@163.com> Message-ID: Dear Wen Dawei, Thanks a lot for letting us know about this issue. We are currently performing server maintenance, thus this issue must be because of that. I will look into it ASAP and let you know once it's fixed. Best wishes, Andrius Merkys On 2020-01-09 13:40, Wen Dawei wrote: > Hello, > > I have been using COD for years and I feel grateful for the works. > Recently, I found a problem when I tried to search some crystal > structure in COD. > For example, when I tried to search "NaCl" (or something like > "Al2O3"), but the system told me "there are no files matching your > search criteria". That's strange. > I have never met such problem before. Is there anything with my input > or there are bugs in recent version of COD? > (For the conditions, please see the appendix files. I failed no matter > I filled the "number of distinct elements min and max" or not.) > > Best regards. > > > -- > Jiangmen, Guangdong, 529020, China > Wuyi University > School of Applied Physics and Materials > Dawei Wen > > ???????? > ???? > ????????? > ??? > > > ? > > > -- > 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. Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 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 merkys at ibt.lt Thu Jan 9 14:21:11 2020 From: merkys at ibt.lt (Andrius Merkys) Date: Thu, 9 Jan 2020 14:21:11 +0200 Subject: [Cod-bugs] Problem: fail to search anything In-Reply-To: <3ae58c9d.8e21.16f8a1ac44a.Coremail.ontaii@163.com> References: <3ae58c9d.8e21.16f8a1ac44a.Coremail.ontaii@163.com> Message-ID: <3470bf1e-2522-5935-fbab-060be9d8f21a@ibt.lt> Dear Wen Dawei, I have just fixed the issue. Now the search for "NaCl" returns 34 entries, as expected. Thanks again for reporting the problem! Best wishes, Andrius Merkys On 2020-01-09 13:40, Wen Dawei wrote: > Hello, > > I have been using COD for years and I feel grateful for the works. > Recently, I found a problem when I tried to search some crystal > structure in COD. > For example, when I tried to search "NaCl" (or something like > "Al2O3"), but the system told me "there are no files matching your > search criteria". That's strange. > I have never met such problem before. Is there anything with my input > or there are bugs in recent version of COD? > (For the conditions, please see the appendix files. I failed no matter > I filled the "number of distinct elements min and max" or not.) > > Best regards. > > > -- > Jiangmen, Guangdong, 529020, China > Wuyi University > School of Applied Physics and Materials > Dawei Wen > > ???????? > ???? > ????????? > ??? > > > ? > > > -- > 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. Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 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 merkys at ibt.lt Fri Jan 10 17:11:08 2020 From: merkys at ibt.lt (Andrius Merkys) Date: Fri, 10 Jan 2020 17:11:08 +0200 Subject: [Cod-bugs] Question about COD In-Reply-To: References: Message-ID: Dear Abelardo, The COD IDs currently are assigned to CIF files by the journal of their publication, according to the following table: start_id??? end_id??? journal 2100000??? 2199999??? Acta Cryst. Section B 2200000??? 2299999??? Acta Cryst. Section E 2000000??? 2099999??? Acta Cryst. Section C 1000000??? 1999999??? other journals 2300000??? 2309999??? J. Appl. Cryst. 4000000??? 4019999??? Chemistry of Materials 4020000??? 4059999??? Journal of Organic Chemistry 4060000??? 4099999??? Organometallics 4100000??? 4299999??? JACS 4300000??? 4499999??? Inorganic Chemistry 5000000??? 5001999??? Reciprocal Net 5900000??? 5999999??? historic structures 6000000??? 6199999??? structures from REFs w/o coord. 7700000??? 7999999??? Dalton Trans. 7050000??? 7099999??? New Journal of Chemistry 7100000??? 7149999??? Chem. Comm. 7150000??? 7199999??? Organic & Biomolecular Chemistry 8000000??? 8099999??? Chemistry Letters 9000000??? 9999999??? AMCSD 2310000??? 2319999??? Acta Crystallographica 8100000??? 8199999??? Zeitschrift f?r Kristallographie 7200000??? 7699999??? other RSC journals 4500000??? 4999999??? other ACS journals 3000000??? 3499999??? prepublication web depositions 3500000??? 3999999??? personal communications to COD However, this assignment is subject to change in the future. Hope this helps, Andrius On 2020-01-07 01:27, Abelardo M. Silva wrote: > > You are organizing the data in directories with root names 1 to 9.? > What is the selection criteria for the type of molecules stored in > each of them? > -- Dr. Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 LT-10257 Vilnius, Lithuania -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From grazulis at ibt.lt Sat Jan 11 13:19:01 2020 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Sat, 11 Jan 2020 13:19:01 +0200 Subject: [Cod-bugs] COD conversion with HighScore In-Reply-To: References: Message-ID: Dear Thomas, On 2020-01-08 18:22, Thomas Dortmann wrote: > Thanks a lot for your letters and explanations. I'm sorry that it > took a while to discuss your input and write this answer. No problem, your answer is really fast! > One problem is the CIF syntax, which allows for a lot of freedom (= > better readability), but must not be unique, when interpreted by > software. Unfortunately this will not change, and for sure not for > already existing CIFs. Indeed, CIF is harder to parse than line-based Unix tool formats. That's why I would recommend using a full-featured CIF parser. We actually have a quite decent F/LOSS parser in our cod-tools that works with C/C++, Perl and Python ;) IMHO, some complexity is unavoidable if we want to parse unambiguously the data produced by different people at different times. The format needs to be specified mathematically (CIF is); more simple formats like CSV actually cause more problems in a longs... Two notes on atomic coordinates: In the list you have sent (COD/COD_Conv_Warnings.xlsx), a number of entries contain warning 'No element found for atom:,"""?"""' As you probably know, technically, this is not and error in the COD or in the CIF, since a lone question mark, '?' (without the quotes), is permissible as a token for any value (including coordinates or Uij!). COD currently stores a small number of structures for which we do not have the coordinates; we can not get these coordinates mostly because structures are behind paywalls. We prefer to keep this records with the '?' coordinates so that we know these structures were published, so we can search for them if that opportunity arises. Structures without coordinates are easy to filter Another important warning is 'No element found for atom:,"""."""'. Now, these dots there are for a good reason: most of such entries were detected to be a fraud at some stage, and were retracted after a careful investigation! The details are specified in each such CIF file from the COD. You should filter away these structures and not use them. They are also marked with '_cod_error_flag retracted' and with the corresponding status and flag columns in the COD SQL DB. We can not simply remove these entries from the COD since robots or people would re-deposit them again, and, even worse, the retraction notice might go unnoticed. They are also a good reminder of what happened, and a good indicator of the publication status (if you download the original CIFs from the publisher's site, they are not marked in any way; a retraction note is for the paper and is posted as "correction") > Converting the CIFs from the COD (to generate peak lists and profiles > for search-match), we experience the following problems: > > 1. atom_names are not translated correctly into atom_symbols: We > already correct most from your list of 33900 entries, only the "Wat" > name was missing and got translated into "At". This is fixed now, but > we would really prefer to find correct atom_symbols in all CIFs. > > Still there is a number of CIFs where the atom_names are not > interpreted: 1235 warnings (Btw.: "n" could be either nitrogen or a > multiplier, we are not sure) We can offer the following additional data curation mark-up: - we could convert automatically to a mixed case (like "Ca"), on the COD side, all upper-case and lower-case atom designators that *look* strictly like atom names and are unique after the case conversion. We would add a column _atom_site_type_symbol if it does not exists; if it exists, we would adjust the _atom_type_symbol accordingly. Thus, "RU" would be converted to "Ru", "n" and "cl" would become "N" and "Cl"; I am not sure how to interpret CS (as "Cs" or "C" and "S"; the latter case is rare). We would inspect some, but most probably not all changed entries comparing them to original paper. This would help you to determine atom types in your programs, but *may* in some rare cases introduce incorrect interpretations (that will eventually be corrected, of course). If you have your own heuristics for atom type determination, this *may* break the heuristics in some (rare?) cases. Please let me know if this would be beneficial for you, and if the risk of introducing temporary errors is acceptable. If you say yes, we do the conversion and commit. If you say no, we do the conversion slowly, in the background, converting and checking each structure one-by-one. So, for example, I fixed atom types in the COD 4062572 from the list you have sent me, by manually editing the supplement file and redepositing it from the source (along with the other structures from the same paper). > 2. Anisotropic displacement parameters are way too big; often > isotropic values don't match anisotropic values in these cases: We > convert from Us or Betas to Bs; the warning identifies one or more > Bansio values >= 10. This results in wrong phase quantitations with > the Rietveld method. (We also recalculate Biso from the Banisos, when > Biso is missing) This is the biggest group of CIFs generating > warnings during the conversion: 123.717 warnings This is an interesting issue, I'll write a separate letter on this. > 3. invalid space group: 454 CIFs I think at the moment most space-groups that could be corrected are corrected. Please not that some CIFs use non-standard settings; the best think is IMHO to parse symmetry operators when they exist and use them instead of interpreting the spacegroup symbols. Some structures from your list are also modulated structures with super-spacegroups. We'll see how many entries from the list can be corrected, but probably not all. > You find a list of all CIFs throwing warnings during conversion in > the attached Excel sheet, ordered by the type of warning and the COD > ID number. I hope this will help to correct errors in the COD and to > make it better applicable through time. Please let me know when you > need more information, or want additional checks during our > conversions to find out more details. Thanks, I went through the list and will send you some remarks in the next e-mail; the remarks on '.' and '?' coordinates are above. > Discussing things with my boss it looks like we are not going to put > real effort (like paying a student) into this, because this would > help the competition as well. I see your point. The list of issues you have sent us is very useful for us, and we'll fix the things that we can fix. Sincerely, Saulius -- 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From grazulis at ibt.lt Sat Jan 11 16:26:01 2020 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Sat, 11 Jan 2020 16:26:01 +0200 Subject: [Cod-bugs] COD conversion with HighScore In-Reply-To: References: Message-ID: <302131fd-91c5-7fde-1425-25711c20462d@ibt.lt> Hi, Thomas, these are my thoughts regarding Biso and Uiso. On 2020-01-08 18:22, Thomas Dortmann wrote: > Please let me know when you need more information, or want additional > checks during our conversions to find out more details. I have written a small Perl program to calculate Ueq and Beq from the Uij, and to output it along with the CIFs Uiso version (http://saulius-grazulis.lt/~saulius/.e6be37a23b470b0ded2e36c9d9a15ba529de29e9/). I have calculated Ueq and Beq from the Uij tensors for all structures that were marked as having 'Large (>= 10) Banis values' in your list. Do I correctly understand that the first number, r.g. 51 in ': 51; No. of atoms: 289', is the number of atoms that have Beq > 10? If so, for some reason I get slightly smaller values than you; for example, for the 1000001 COD structure, I get only 13 such values from U_ij records; with isotropic atoms (hydrogens), I get 141 atoms... Could you please send my your code example (maybe as a pseudo-code) how you calculate the Ueq? I admit that I am not sure if my understanding of the CIF's Uij is correct. I consulted both Fischer1988 (10.1107/S0108270187012745) and Grosse-Kunstleve2002 (10.1107/S0021889802008580), but I am still not sure if I get orthogonalisation correctly. Uij needs to be on orthogonal basis before taking the Tr(Uij) and getting Ueq = (1/3)*Tr(Uij); however, all orthogonalisations which I derive myself or pick from the papers are equivalent to just summing up the U_ii from the CIF: Ueq = (U11 + U22 + U33)/3 I suspect also that the definition on the IUCr page (https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_U_iso_or_equiv.html) is incorrect, the a values should be vectors, and not vector lengths, as stated, and they should form an (aj,aj) scalar product... (?!). I did not yet check the Tables. What formula do you use? In any case, with this method I get values close to those presented in CIFs (mostly within the error margins), and reasonable Beq values. Thus I decided to move on, leaving derivation of the maths for later times :). > 2. Anisotropic displacement parameters are way too big; often > isotropic values don't match anisotropic values in these cases: We > convert from Us or Betas to Bs; the warning identifies one or more > Bansio values >= 10. This results in wrong phase quantitations with > the Rietveld method. (We also recalculate Biso from the Banisos, > when Biso is missing) This is the biggest group of CIFs generating > warnings during the conversion: 123.717 warnings As for the absolute values of Uiso or Biso, I have no special opinion, but I do not spot any big trouble either. Taking a random structure from your list: > #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff > 7225385 C42 0.213 0.212333 16.7652 0.000666667 > 7225385 C41 0.159 0.158667 12.5278 0.000333333 > 7225385 O53 0.134 0.133667 10.5539 0.000333333 > 7225385 O43 0.1237 0.123667 9.76433 3.33333e-05 So the largest Beq is 16.8 ?^2, next one is 12.5 ?^2, and starting from the fourth atom they are below 10. In many random structures I observe *all* Beq < 10, and all values seem consistent across the files and not too much scattered. Granted, some B values are very large, over the 100, but so that authors reported them. I do not see any way to rectify this short of resolving the structure from a better crystal... In many structures, there are just few such atoms with large Biso values, and they are often in disordered regions; Beq from ordered regions look normal to me, e.g.: > saulius at varanas Uiso/ $ cod-download -s 7120853 | ./cif_Uiso | sort -gr -k4,4 | head -n 4 > C25B 2.119 2.00067 157.966 0.118333 > C19B 1.149 2 157.914 -0.851 > C26B 1.163 1.986 156.808 -0.823 > C6 1.13 1.95833 154.624 -0.828333 > saulius at varanas Uiso/ $ cod-download -s 7120853 | ./cif_Uiso | sort -gr -k4,4 | tail -n 8 > C41A 0.035 0.0373333 2.94772 -0.00233333 > C32A 0.037 0.0373333 2.94772 -0.000333333 > C30A 0.036 0.031 2.44766 0.005 > C29A 0.037 0.0356667 2.81613 0.00133333 > #SPCGRP : P -1 > #FILENAME : - > #DATABLCK : 7120853 > #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff Thus, the largest B-factors are 158, but they are on a periphery of a flexible organic group here; the core atoms have much lower Bs. Coming from a protein crystallography side, such situation does not seem to me as something extraordinary. Granted, B=160 is too much, but to me this just means that the crystal was rather disordered (in that region?), or the given part of the molecule was not modelled well (the contrast of B-factors in this particular entry is quite high). Maybe constraints should have been applied during refinement. Given that this is a published structure from a (reputable?) chemical journal (https://doi.org/10.1039/C7CC06797F), I do not see how we can do much about this, except excluding such structures from computations (but we will probably loose a lot of data this way). Such is the state of the art in the chemical crystallography field (?). > You find a list of all CIFs throwing warnings during conversion in > the attached Excel sheet, ordered by the type of warning and the COD > ID number. I hope this will help to correct errors in the COD and to > make it better applicable through time. What I agree to be a clear sign of technical problem is a large discrepancy between Ueq (calculated from the Uij tensor) an and the Uiso or Biso provided by the authors. I have spotted in the list that you have provided: 18 structures with at least one Uiso-Ueq value > 1.0; 12 structures with at least one Uiso-Ueq value < -10.0; Most structures in these lists are *consistently* too high or too low; only two COD IDs in this list have atoms not in these extreme ranges. The 16 of the structures from the 'Uiso-Ueq > 1.0' list seem to have Beq specified instead of Ueq, since the value is approx. x80 too large; when corrected with this assumption, the values become reasonable and consistent: > #DATABLCK : 4321814 > #SPCGRP : C m c 21 > #CELL : 11.889 33.380 9.012 90 90 90 > #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff > CU1 2.5 0.0316667 2.5003 2.46833 > CU2 2.9 0.0366667 2.89508 2.86333 > CU3 3 0.038 3.00036 2.962 > CU4 2.9 0.0366667 2.89508 2.86333 > CU5 2.91 0.037 2.9214 2.873 As you see, Uiso in the CIF is nearly exactly the same as the Beq calculated by my script from the Uij values. I suggest fixing these structures by renaming the data name: s/_atom_site_U_iso_or_equiv/_atom_site_B_iso_or_equiv/; vis.: > saulius at varanas Uiso/ $ cod-download -s 4321814 | sed 's/_atom_site_U_iso_or_equiv/_atom_site_B_iso_or_equiv/' | ./cif_Uiso > #FILENAME : - > #DATABLCK : 4321814 > #SPCGRP : C m c 21 > #CELL : 11.889 33.380 9.012 90 90 90 > #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff > CU1 0.0316629 0.0316667 2.5003 -3.79678e-06 > CU2 0.0367289 0.0366667 2.89508 6.22624e-05 > CU3 0.0379954 0.038 3.00036 -4.55613e-06 > CU4 0.0367289 0.0366667 2.89508 6.22624e-05 > CU5 0.0368556 0.037 2.9214 -0.000144419 The table above shows that after this renaming Uiso(CIF) (computed from the corresponding _B_iso_or_equiv value in the incoming CIF) are again the same as the Ueq computed from the Uij tensor. The 12 structures with enormous negative differences have, IMHO, a scale problem in the Uij fields; probably the authors provided values Uij * 10^4 or something like that (such conventions were usual in papers or in old computer printouts during 90-ies). If we find the clear indication of such scaling in the corresponding papers, we can correct the problem, otherwise the Uij data is lost... I have inspected one such IUCr paper, and the authors, unfortunately, do not mention their scaling convention at all. We'll have to check the others. One structure, I have noticed, has too little values for hydrogen ('H') Uij fields, but, by accident, the number of column in the loop matches. This will be picked up by our validator which Antanas has written (we now need to send away a paper about the validator, and then we can dig deeper into the COD corrections). My proposals of the corrections are noted in the .csv file on my home page (http://saulius-grazulis.lt/~saulius/.aa50f94063d8810bf957e3b39f733acd7474bc08/COD_Conv_Warnings_FIXES.csv), based on your list. Of course we'll scan the rest of the COD as well, as soon as I am sure that I compute Ueq's correctly :). Sincerely, Saulius -- 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From grazulis at ibt.lt Sat Jan 11 16:30:52 2020 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Sat, 11 Jan 2020 16:30:52 +0200 Subject: [Cod-bugs] COD conversion with HighScore In-Reply-To: References: Message-ID: <5e006215-23fc-b2b5-8cdd-f1ae037c1df7@ibt.lt> On 2020-01-08 18:22, Thomas Dortmann wrote: > This is the biggest group of CIFs generating warnings during the conversion: 123.717 warnings One more note: during the processing of the files from your list, I get a number of warnings about non-numeric values (e.g. "Argument "0.05147(16" isn't numeric ...") when computing Ueq. There are 101 such warnings in my logs. This is a correctable bug in COD CIFs (mostly introduced by the original publication...); we plan to fix them all systematically since such typos are spotted by our new validator :). Regards, Saulius -- 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From grazulis at ibt.lt Sat Jan 11 17:42:30 2020 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Sat, 11 Jan 2020 17:42:30 +0200 Subject: [Cod-bugs] COD conversion with HighScore In-Reply-To: References: Message-ID: Dear Thomas, I have just fixed a stupid bug in my cif_Uiso script (the script would not get cell angles other than 90 degrees). Now the agreement between Uiso(CIF) and Ueq is better :). Also, I now see why my orthogonalisation did not work. I will recalculate the tables. On 2020-01-03 15:30, Thomas Dortmann wrote: > 2. We check the values of Biso and Baniso, and we also convert > Baniso-values back to Biso values; > > in COD entry 9014636 there are very big Uaniso-values (converted into > Baniso values > 10), but small Uiso-values? I think my code now shows what you mean: > saulius at varanas Uiso/ $ cod-download -s 9014636 | ./cif_Uiso > #DATABLCK : 9014636 > #SPCGRP : C 1 2/m 1 > #CELL : 9.3720 17.6312 5.2732 90 102.247 90 > #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff > NaA 0.04154 0.416959 32.9218 -0.375419 > NaAm 0.03002 0.299077 23.6142 -0.269057 > LiM4 0.02014 0.20043 15.8253 -0.18029 > NaM4 0.02014 0.20043 15.8253 -0.18029 > CaM4 0.02014 0.20043 15.8253 -0.18029 > MgM1 0.00684 0.0720588 5.68954 -0.0652188 > FeM1 0.00684 0.0720588 5.68954 -0.0652188 > ZnM1 0.00684 0.0720588 5.68954 -0.0652188 > AlM2 0.00532 0.0504816 3.98587 -0.0451616 I am not sure why this is so. Unfortunately, the original paper has no accompanying CIF, and I can not get the original paper. I'll ask Bob Downs what they did with this structure. Could be a typo. > Questions: does the COD apply a sanity check on the supplied B (or U) > values, and do you compare anisotropic with isotropic values? So, the answer now is: we start do do this, with your help ;). However, in case if discrepancies in the published structures, we can probably only flag them, but not correct ? unless the authors provide a re-refined version. Regards, Saulius -- 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. From thomas.degen at panalytical.com Sat Jan 11 18:47:32 2020 From: thomas.degen at panalytical.com (Thomas Degen) Date: Sat, 11 Jan 2020 16:47:32 +0000 Subject: [Cod-bugs] COD conversion with HighScore In-Reply-To: <302131fd-91c5-7fde-1425-25711c20462d@ibt.lt> References: <302131fd-91c5-7fde-1425-25711c20462d@ibt.lt> Message-ID: Hi Saulius, >, is the number of atoms that have Beq > 10? No, it is what it says, it is about how often any of the anisotropic values (B11,B22,B33,B12,B23,B13) hit the "B >= 10" limit. We are using B instead of U in the UI because these values are closer to 1, which makes them more convenient to look at. > Could you please send my your code example This is approximately the code to convert Banis to Biso: case FSpaceGroup.SimpleCrystalSystem of scTriclinic: begin Atom.Biso.Value := (1 / 3) * (Atom.b11.Value * Sqr(Cell.a * ReciprocalCell.a) + Atom.b22.Value * Sqr(Cell.b * ReciprocalCell.b) + Atom.b33.Value * Sqr(Cell.c * ReciprocalCell.c) + 2 * Atom.b12.Value * Cell.a * Cell.b * ReciprocalCell.a * ReciprocalCell.b * CosDeg(Cell.gamma) + 2 * Atom.b13.Value * Cell.a * Cell.c * ReciprocalCell.a * ReciprocalCell.c * CosDeg(Cell.beta) + 2 * Atom.b23.Value * Cell.b * Cell.c * ReciprocalCell.b * ReciprocalCell.c * CosDeg(Cell.alpha)); end; scMonoclinic: begin case FSpaceGroup.SpaceGroupInfo._MonoclinicAxis of enmMonoclinicAxis.maB: Atom.Biso.Value := (1 / 3) * (Atom.b22.Value + 1 / Sqr(SinDeg(Cell.Beta)) * (Atom.b11.Value + Atom.b33.Value + 2 * Atom.b13.Value * CosDeg(Cell.Beta))); enmMonoclinicAxis.maC: Atom.Biso.Value := (1 / 3) * (Atom.b33.Value + 1 / Sqr(SinDeg(Cell.Gamma)) * (Atom.b11.Value + Atom.b22.Value + 2 * Atom.b12.Value * CosDeg(Cell.Gamma))); enmMonoclinicAxis.maA: Atom.Biso.Value := (1 / 3) * (Atom.b11.Value + 1 / Sqr(SinDeg(Cell.Alpha)) * (Atom.b11.Value + Atom.b11.Value + 2 * Atom.b23.Value * CosDeg(Cell.Alpha))); end; end; scOrthorhombic, scTetragonal, scCubic: Atom.Biso.Value := (1 / 3) * (Atom.b11.Value + Atom.b22.Value + Atom.b33.Value); scTrigonalRhombAxes: Atom.Biso.Value := (1 / 3) * (Sqr(Cell.a * ReciprocalCell.a) * (Atom.b11.Value + Atom.b22.Value + Atom.b33.Value + 2 * CosDeg(Cell.Alpha) * (Atom.b12.Value + Atom.b13.Value + Atom.b23.Value))); scHexagonal, scTrigonalHexAxes: Atom.Biso.Value := (1 / 3) * (Atom.b33.Value + (4 / 3) * (Atom.b11.Value + Atom.b22.Value - Atom.b12.Value)); end; Atom.Biso.Deviation := ((Atom.b11.Deviation + Atom.b22.Deviation + Atom.b33.Deviation) / 3) * (1 / 6); end; Concerning these many pattern having so many big displacement parameters (which we don't see in other databases) My guess is that the Units got confused. So it wasn?t U but the data was given as B or Beta instead (and simply wrongly flagged as U). Best regards, Thomas -----Original Message----- From: Saulius Gra?ulis Sent: Saturday, January 11, 2020 3:26 PM To: Thomas Dortmann ; Thomas Degen ; cod-bugs at ibt.lt Cc: Thomas Dortmann Subject: Re: [Cod-bugs] COD conversion with HighScore Hi, Thomas, these are my thoughts regarding Biso and Uiso. On 2020-01-08 18:22, Thomas Dortmann wrote: > Please let me know when you need more information, or want additional > checks during our conversions to find out more details. I have written a small Perl program to calculate Ueq and Beq from the Uij, and to output it along with the CIFs Uiso version (http://saulius-grazulis.lt/~saulius/.e6be37a23b470b0ded2e36c9d9a15ba529de29e9/). I have calculated Ueq and Beq from the Uij tensors for all structures that were marked as having 'Large (>= 10) Banis values' in your list. Do I correctly understand that the first number, r.g. 51 in ': 51; No. of atoms: 289', is the number of atoms that have Beq > 10? If so, for some reason I get slightly smaller values than you; for example, for the 1000001 COD structure, I get only 13 such values from U_ij records; with isotropic atoms (hydrogens), I get 141 atoms... Could you please send my your code example (maybe as a pseudo-code) how you calculate the Ueq? I admit that I am not sure if my understanding of the CIF's Uij is correct. I consulted both Fischer1988 (10.1107/S0108270187012745) and Grosse-Kunstleve2002 (10.1107/S0021889802008580), but I am still not sure if I get orthogonalisation correctly. Uij needs to be on orthogonal basis before taking the Tr(Uij) and getting Ueq = (1/3)*Tr(Uij); however, all orthogonalisations which I derive myself or pick from the papers are equivalent to just summing up the U_ii from the CIF: Ueq = (U11 + U22 + U33)/3 I suspect also that the definition on the IUCr page (https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_U_iso_or_equiv.html) is incorrect, the a values should be vectors, and not vector lengths, as stated, and they should form an (aj,aj) scalar product... (?!). I did not yet check the Tables. What formula do you use? In any case, with this method I get values close to those presented in CIFs (mostly within the error margins), and reasonable Beq values. Thus I decided to move on, leaving derivation of the maths for later times :). > 2. Anisotropic displacement parameters are way too big; often > isotropic values don't match anisotropic values in these cases: We > convert from Us or Betas to Bs; the warning identifies one or more > Bansio values >= 10. This results in wrong phase quantitations with > the Rietveld method. (We also recalculate Biso from the Banisos, when > Biso is missing) This is the biggest group of CIFs generating warnings > during the conversion: 123.717 warnings As for the absolute values of Uiso or Biso, I have no special opinion, but I do not spot any big trouble either. Taking a random structure from your list: > #@ label Uiso(CIF)Ueq(comp)Beq(comp)diff > 7225385C42 0.213 0.212333 16.7652 0.000666667 > 7225385C41 0.159 0.158667 12.5278 0.000333333 > 7225385O53 0.134 0.133667 10.5539 0.000333333 > 7225385O43 0.1237 0.123667 9.76433 3.33333e-05 So the largest Beq is 16.8 ?^2, next one is 12.5 ?^2, and starting from the fourth atom they are below 10. In many random structures I observe *all* Beq < 10, and all values seem consistent across the files and not too much scattered. Granted, some B values are very large, over the 100, but so that authors reported them. I do not see any way to rectify this short of resolving the structure from a better crystal... In many structures, there are just few such atoms with large Biso values, and they are often in disordered regions; Beq from ordered regions look normal to me, e.g.: > saulius at varanas Uiso/ $ cod-download -s 7120853 | ./cif_Uiso | sort -gr -k4,4 | head -n 4 > C25B 2.119 2.00067 157.966 0.118333 > C19B 1.149 2 157.914 -0.851 > C26B 1.163 1.986 156.808 -0.823 > C6 1.13 1.95833 154.624 -0.828333 > saulius at varanas Uiso/ $ cod-download -s 7120853 | ./cif_Uiso | sort -gr -k4,4 | tail -n 8 > C41A 0.035 0.0373333 2.94772 -0.00233333 > C32A 0.037 0.0373333 2.94772-0.000333333 > C30A 0.036 0.031 2.44766 0.005 > C29A 0.037 0.0356667 2.81613 0.00133333 > #SPCGRP :P -1 > #FILENAME :- > #DATABLCK :7120853 > #@ label Uiso(CIF)Ueq(comp)Beq(comp)diff Thus, the largest B-factors are 158, but they are on a periphery of a flexible organic group here; the core atoms have much lower Bs. Coming from a protein crystallography side, such situation does not seem to me as something extraordinary. Granted, B=160 is too much, but to me this just means that the crystal was rather disordered (in that region?), or the given part of the molecule was not modelled well (the contrast of B-factors in this particular entry is quite high). Maybe constraints should have been applied during refinement. Given that this is a published structure from a (reputable?) chemical journal (https://doi.org/10.1039/C7CC06797F), I do not see how we can do much about this, except excluding such structures from computations (but we will probably loose a lot of data this way). Such is the state of the art in the chemical crystallography field (?). > You find a list of all CIFs throwing warnings during conversion in the > attached Excel sheet, ordered by the type of warning and the COD ID > number. I hope this will help to correct errors in the COD and to make > it better applicable through time. What I agree to be a clear sign of technical problem is a large discrepancy between Ueq (calculated from the Uij tensor) an and the Uiso or Biso provided by the authors. I have spotted in the list that you have provided: 18 structures with at least one Uiso-Ueq value > 1.0; 12 structures with at least one Uiso-Ueq value < -10.0; Most structures in these lists are *consistently* too high or too low; only two COD IDs in this list have atoms not in these extreme ranges. The 16 of the structures from the 'Uiso-Ueq > 1.0' list seem to have Beq specified instead of Ueq, since the value is approx. x80 too large; when corrected with this assumption, the values become reasonable and consistent: > #DATABLCK :4321814 > #SPCGRP :C m c 21 > #CELL :11.88933.3809.012909090 > #@ label Uiso(CIF)Ueq(comp)Beq(comp)diff > CU1 2.5 0.0316667 2.5003 2.46833 > CU2 2.9 0.0366667 2.89508 2.86333 > CU3 3 0.038 3.00036 2.962 > CU4 2.9 0.0366667 2.89508 2.86333 > CU5 2.91 0.037 2.9214 2.873 As you see, Uiso in the CIF is nearly exactly the same as the Beq calculated by my script from the Uij values. I suggest fixing these structures by renaming the data name: s/_atom_site_U_iso_or_equiv/_atom_site_B_iso_or_equiv/; vis.: > saulius at varanas Uiso/ $ cod-download -s 4321814 | sed 's/_atom_site_U_iso_or_equiv/_atom_site_B_iso_or_equiv/' | ./cif_Uiso > #FILENAME :- > #DATABLCK :4321814 > #SPCGRP :C m c 21 > #CELL :11.88933.3809.012909090 > #@ label Uiso(CIF)Ueq(comp)Beq(comp)diff > CU1 0.0316629 0.0316667 2.5003-3.79678e-06 > CU2 0.0367289 0.0366667 2.89508 6.22624e-05 > CU3 0.0379954 0.038 3.00036-4.55613e-06 > CU4 0.0367289 0.0366667 2.89508 6.22624e-05 > CU5 0.0368556 0.037 2.9214-0.000144419 The table above shows that after this renaming Uiso(CIF) (computed from the corresponding _B_iso_or_equiv value in the incoming CIF) are again the same as the Ueq computed from the Uij tensor. The 12 structures with enormous negative differences have, IMHO, a scale problem in the Uij fields; probably the authors provided values Uij * 10^4 or something like that (such conventions were usual in papers or in old computer printouts during 90-ies). If we find the clear indication of such scaling in the corresponding papers, we can correct the problem, otherwise the Uij data is lost... I have inspected one such IUCr paper, and the authors, unfortunately, do not mention their scaling convention at all. We'll have to check the others. One structure, I have noticed, has too little values for hydrogen ('H') Uij fields, but, by accident, the number of column in the loop matches. This will be picked up by our validator which Antanas has written (we now need to send away a paper about the validator, and then we can dig deeper into the COD corrections). My proposals of the corrections are noted in the .csv file on my home page (http://saulius-grazulis.lt/~saulius/.aa50f94063d8810bf957e3b39f733acd7474bc08/COD_Conv_Warnings_FIXES.csv), based on your list. Of course we'll scan the rest of the COD as well, as soon as I am sure that I compute Ueq's correctly :). Sincerely, Saulius -- 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 email and any files transmitted with it are confidential and maybe legally privileged. Such message is intended solely for the use of the individual or entity to whom they are addressed. Please notify the originator of the message if you are not the intended recipient and destroy all copies of the message. Please note that any use, dissemination, or reproduction is strictly prohibited and may be unlawful. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From grazulis at ibt.lt Sun Jan 12 19:01:23 2020 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Sun, 12 Jan 2020 19:01:23 +0200 Subject: [Cod-bugs] COD conversion with HighScore In-Reply-To: References: <302131fd-91c5-7fde-1425-25711c20462d@ibt.lt> Message-ID: <60427be7-9b95-2725-af7c-90341b201eeb@ibt.lt> Dear Thomas, thank you for the clarifications! On 2020-01-11 18:47, Thomas Degen wrote: > No, it is what it says, it is about how often any of the anisotropic values (B11,B22,B33,B12,B23,B13) hit the "B >= 10" limit. I see. I misread the table, assuming 'Banis' is in fact Beq computed from Bij. Now I can mostly get the same counts as in your table; occasionally I still get somewhat less Bij >= 10 as in your table (e.g. for COD 7123444 I get 51 large Bij value instead of 54). But the results are now very similar, so I can proceed with the survey of the issues. Do you take Bij values after transforming them to an orthogonal frame, or in the original CIF Uij frame of reference? > We are using B instead of U in the UI because these values are closer to 1, which makes them more convenient to look at. OK, clear. * 8 * pi ** 2 ? >> Could you please send my your code example > This is approximately the code to convert Banis to Biso: > > case FSpaceGroup.SimpleCrystalSystem of > scTriclinic: > begin > Atom.Biso.Value := (1 / 3) * > (Atom.b11.Value * Sqr(Cell.a * ReciprocalCell.a) + Atom.b22.Value * Sqr(Cell.b * ReciprocalCell.b) > + Atom.b33.Value * Sqr(Cell.c * ReciprocalCell.c) > + 2 * Atom.b12.Value * Cell.a * Cell.b * ReciprocalCell.a * ReciprocalCell.b * CosDeg(Cell.gamma) > + 2 * Atom.b13.Value * Cell.a * Cell.c * ReciprocalCell.a * ReciprocalCell.c * CosDeg(Cell.beta) > + 2 * Atom.b23.Value * Cell.b * Cell.c * ReciprocalCell.b * ReciprocalCell.c * CosDeg(Cell.alpha)); > end; Perfect. This is the same formula as Fischer1988 describes, and which I use as well. The values should be reproducible (even though I do not use special cases for higher-symmetry groups). > Concerning these many pattern having so many big displacement parameters (which we don't see in other databases) > My guess is that the Units got confused. So it wasn?t U but the data was given as B or Beta instead (and simply wrongly flagged as U). In some cases, the unites are indeed mixed up, but I now find a bunch of other reasons. I'll let you know in a follow-up mail. Sincerely yours, Saulius -- 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From grazulis at ibt.lt Sun Jan 12 20:59:18 2020 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Sun, 12 Jan 2020 20:59:18 +0200 Subject: [Cod-bugs] COD conversion with HighScore In-Reply-To: References: <302131fd-91c5-7fde-1425-25711c20462d@ibt.lt> Message-ID: <2f3c2a79-5504-5a60-c867-ab16e7981c97@ibt.lt> Dear Thomas, Below are my ideas regarding high Bij values. On 2020-01-11 18:47, Thomas Degen wrote: > Concerning these many pattern having so many big displacement > parameters (which we don't see in other databases) > My guess is that the Units got confused. So it wasn?t U but the data > was given as B or Beta instead (and simply wrongly flagged as U). This is indeed sometimes the case, but not always. -- 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. From grazulis at ibt.lt Sun Jan 12 21:08:32 2020 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Sun, 12 Jan 2020 21:08:32 +0200 Subject: [Cod-bugs] COD conversion with HighScore In-Reply-To: <2f3c2a79-5504-5a60-c867-ab16e7981c97@ibt.lt> References: <302131fd-91c5-7fde-1425-25711c20462d@ibt.lt> <2f3c2a79-5504-5a60-c867-ab16e7981c97@ibt.lt> Message-ID: <92d3ce70-d4b0-286c-6985-d58c9d1805f3@ibt.lt> Sorry for the previous letter ? I hit "Send" instead of "Save"... to make long story short, I attach to preliminary surveys of mine with various problems spotted with the Uij values. I examined those that have Bij > 300 ;) I hope the files will make sense to you; I can comment on them later if needed. As for them bulk of Bij > 10 structures (more than 100 thous. COD entries!): IMHO, most are legit structures. COD has a lot of organics, and a lot of large molecules; so B ~ 10.0 does not sound wild to me. I would expect: for small, inorganic, very good quality single crystals, minerals, smal unit cells (B units ? ?^2, 8*Pi^2 factor included): B between 1 and 5 (but I have little experience here, just guessing from what I seen in the COD and in publications); thus, in the ICSD average Bij values are expected to be significantly smaller than in the COD :) For organics, large molecules: B between 5 and 50 (but again, I have little experience here, just guessing from what I seen in the COD and in publications); for proteins, nucleic acids: B between 20 and 100 (experience with protein crystallography and PDB). Does this sound very wild to you? :) Regards, Saulius On 2020-01-12 20:59, Saulius Gra?ulis wrote: > Dear Thomas, > > Below are my ideas regarding high Bij values. > > On 2020-01-11 18:47, Thomas Degen wrote: >> Concerning these many pattern having so many big displacement >> parameters (which we don't see in other databases) > >> My guess is that the Units got confused. So it wasn?t U but the data >> was given as B or Beta instead (and simply wrongly flagged as U). > > This is indeed sometimes the case, but not always. > -- 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 -------------- 2010272 S.G. Bij instead of Uij 1544873 S.G. Reason for large Uij not clear at all. 1544907 S.G. Reason for large Uij not clear at all. Similar to 1544873 2006293 S.G. Bij instead of Uij 2006294 S.G. Bij instead of Uij 2006295 S.G. Bij instead of Uij 2009417 S.G. Biso instead of Uiso. Bad scale on Uij 2009425 S.G. Bad scale on Uij 2010272 S.G. Bij instead of Uij 4322875 S.G. The first (U11) value on *some*, but not *all*, hydrogens seems to be converted to B instead of U (???) 4061132 S.G. Values for one atom ('C(1)') very large. Problems with refinement? 4114581 S.G. Digits missing from some Uij values? 9009485 S.G. Large negative U23 for some atoms. Problems with refinement? 4115051 S.G. Digits missing from some Uij values? 4115055 S.G. Digits missing from some Uij values? 4115066 S.G. Digits missing from some Uij values? 4116019 S.G. Bij instead of Uij for just one atom? (???) Or refinement problems? 4307487 S.G. Bij instead of Uij for just one atom? (???) Or refinement problems? 4322175 S.G. Digits missing from some Uij values? Problems with refinement? 9004552 S.G. Some atoms seem to have Uij, some probably have Biso specified as U11. Manual data entry error? 9007611 S.G. Heavy atoms seem to have Uij, hydrogens probably have Biso specified as U11. Manual data entry error? 9013813 S.G. Two Uij values stand out. Manual data entry error? (Typed "9" instead of "0"?) 9013821 S.G. One Uij value stands out. Manual data entry error? -------------- next part -------------- #FILENAME : - #DATABLCK : 2001154 Biso instead of Uiso #SPCGRP : I 1 2/a 1 #CELL : 13.0100 9.1620 15.669 90.0 93.251 90.0 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff Mn 2.84 0.0356218 2.81258 2.80438 N1 3.05 0.0383848 3.03074 3.01162 N2 3.78 0.0476335 3.76099 3.73237 N3 3.59 0.0452069 3.5694 3.54479 C1 3.16 0.0398607 3.14727 3.12014 C2 4.34 0.0542711 4.28507 4.28573 C3 5.17 0.0649715 5.12994 5.10503 C4 4.37 0.0557018 4.39804 4.3143 C5 3.35 0.0425196 3.35721 3.30748 C6 4.13 0.0518352 4.09274 4.07816 C7 4.15 0.0524458 4.14096 4.09755 Cl 4.43 0.0558107 4.40664 4.37419 OW 9.9 0.120518 9.51573 9.77948 #FILENAME : - #DATABLCK : 2001156 Biso instead of Uiso #SPCGRP : P n a 21 #CELL : 17.628 10.1680 6.4960 90.0 90.0 90.0 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff Cu 2.509 0.0317867 2.50977 2.47721 Cl1 3.58 0.0454333 3.58727 3.53457 N1 2.08 0.0263333 2.0792 2.05367 N2 3.28 0.0415667 3.28197 3.23843 N3 3.09 0.0390667 3.08458 3.05093 C1 2.18 0.0276667 2.18447 2.15233 C2 2.66 0.0337 2.66085 2.6263 C3 2.78 0.0351667 2.77665 2.74483 C4 2.76 0.0349 2.75559 2.7251 C5 2.33 0.0294667 2.32659 2.30053 C6 2.96 0.0374667 2.95825 2.92253 C7 2.81 0.0356 2.81086 2.7744 Cl2 2.93 0.0370667 2.92667 2.89293 O1 6.9 0.0863333 6.81661 6.81367 O2 10.7 0.135333 10.6855 10.5647 O3 10.6 0.134667 10.6329 10.4653 O4 6.54 0.083 6.55342 6.457 #FILENAME : - #DATABLCK : 2002110 Bad scaling factor #SPCGRP : P 1 21/n 1 #CELL : 7.237 14.952 17.07 90.0 95.11 90.0 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff Ge(1) 213 212.519 16779.8 0.481174 Ge(2) 231 231.539 18281.6 -0.538594 Ge(3) 216 216.68 17108.4 -0.680009 C(1a) 334 332.912 26285.7 1.08832 C(1b) 378 379.611 29972.9 -1.61086 C(2a) 445 444.796 35119.7 0.204079 C(2b) 422 419.279 33104.9 2.72112 C(3a) 437 436.852 34492.5 0.147532 C(3b) 465 466.97 36870.5 -1.97032 C(4) 187 189.92 14995.5 -2.91964 C(5) 202 203.229 16046.3 -1.22913 C(6) 180 179.555 14177.1 0.444861 C(7) 256 253.395 20007.3 2.60508 C(8) 314 315.279 24893.4 -1.27917 C(9) 314 314.5 24831.9 -0.499907 C(10) 279 281.025 22188.8 -2.02463 C(11) 238 241.259 19049 -3.25866 C(12) 304 304.912 24074.9 -0.911856 C(13) 386 386.298 30500.9 -0.298321 #FILENAME : - #DATABLCK : 2003303 Biso instead of Uiso #SPCGRP : P b c a #CELL : 10.716 17.431 35.029 90 90 90 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff Pt 2.78 0.0351667 2.77665 2.74483 Cl 5.2 0.0666667 5.26379 5.13333 P(1) 4.2 0.0523333 4.13207 4.14767 P(2) 3.43 0.0434667 3.43199 3.38653 Si 2.76 0.035 2.76349 2.725 C(10) 4 0.051 4.0268 3.949 C(11) 5.9 0.0753333 5.94808 5.82467 C(12) 8.5 0.109333 8.63261 8.39067 C(13) 12 0.158 12.4752 11.842 C(14) 12 0.156667 12.3699 11.8433 C(15) 7.2 0.0893333 7.05348 7.11067 C(16) 10.5 0.134667 10.6329 10.3653 C(17) 8.5 0.108667 8.57998 8.39133 C(20) 3.7 0.0466667 3.68465 3.65333 C(21) 4.9 0.062 4.89532 4.838 C(22) 6.7 0.085 6.71133 6.615 C(23) 6.9 0.0873333 6.89556 6.81267 C(24) 7.2 0.093 7.34299 7.107 C(25) 5.6 0.071 5.60594 5.529 C(26) 4.9 0.0616667 4.869 4.83833 C(27) 5.5 0.0696667 5.50066 5.43033 C(30) 3.5 0.0446667 3.52674 3.45533 C(31) 4.4 0.056 4.42158 4.344 C(32) 6.1 0.0766667 6.05336 6.02333 C(33) 7.1 0.0896667 7.0798 7.01033 C(34) 6.4 0.0813333 6.42182 6.31867 C(35) 5.1 0.064 5.05324 5.036 C(40) 3.2 0.0406667 3.21091 3.15933 C(41) 4.4 0.0553333 4.36894 4.34467 C(42) 6.8 0.0856667 6.76397 6.71433 C(43) 6.4 0.081 6.3955 6.319 C(44) 6.2 0.0786667 6.21127 6.12133 C(45) 4.4 0.0553333 4.36894 4.34467 C(50) 4.1 0.0516667 4.07944 4.04833 C(51) 6.4 0.081 6.3955 6.319 C(52) 10 0.131333 10.3697 9.86867 C(53) 10 0.131 10.3433 9.869 C(54) 11 0.140667 11.1066 10.8593 C(55) 7.1 0.0903333 7.13243 7.00967 #FILENAME : - #DATABLCK : 2003596 Biso instead of Uiso #SPCGRP : ? #CELL : 12.258 22.289 13.297 90.0 104.64 90.0 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff C1 3.4 0.0423978 3.34759 3.3576 C2 3.8 0.047631 3.76079 3.75237 C3 4.5 0.0571013 4.50854 4.4429 C4 4.9 0.0614476 4.85171 4.83855 C5 4.7 0.0593944 4.6896 4.64061 C6 3.8 0.0482491 3.8096 3.75175 C7 3.5 0.0443292 3.5001 3.45567 C8 3.4 0.0428073 3.37993 3.35719 C9 3.7 0.0462083 3.64846 3.65379 C10 3.8 0.0478708 3.77973 3.75213 C11 4.9 0.0624026 4.92711 4.8376 C12 3.5 0.0449416 3.54845 3.45506 C13 3.7 0.0471451 3.72243 3.65285 C14 3.1 0.0386847 3.05442 3.06132 C15 3.4 0.0425898 3.36276 3.35741 C16 4.4 0.0550877 4.34955 4.34491 C17 4.2 0.0534569 4.22079 4.14654 C18 4.4 0.0558737 4.41161 4.34413 N20 3.8 0.0480272 3.79208 3.75197 C21 4.9 0.0620265 4.89742 4.83797 C22 5.3 0.0674792 5.32794 5.23252 O23 4.7 0.0591038 4.66665 4.6409 C24 5.2 0.0662444 5.23045 5.13376 C25 5.6 0.0713981 5.63737 5.5286 O26 4.7 0.058989 4.65758 4.64101 C27 4.8 0.0608569 4.80507 4.73914 C28 5.1 0.064195 5.06863 5.03581 N30 3.4 0.0429158 3.3885 3.35708 C31 4.2 0.052665 4.15827 4.14733 C32 4.5 0.0571968 4.51608 4.4428 O33 5.3 0.0545653 4.30831 5.24543 C34 7.4 0.0937846 7.40493 7.30622 C35 6.3 0.079495 6.27667 6.22051 O36 5.4 0.0685669 5.41382 5.33143 C37 5.1 0.0639863 5.05215 5.03601 C38 4.8 0.0607167 4.794 4.73928 Cl40 4.4 0.0553309 4.36876 4.34467 O41 7.7 0.0968755 7.64898 7.60312 O42 9.3 0.117287 9.26058 9.18271 O43 5.8 0.073785 5.82583 5.72622 O44 9.1 0.115164 9.09301 8.98484 Cl50 5.9 0.0747503 5.90205 5.82525 O51 14.8 0.187932 14.8385 14.6121 O52 6.4 0.0816635 6.44789 6.31834 O53 11.1 0.1406 11.1013 10.9594 O54 10.4 0.13218 10.4365 10.2678 O60 4.3 0.0550194 4.34416 4.24498 #FILENAME : - #DATABLCK : 2004328 Biso instead of Uiso; bad orthogonalisation? #SPCGRP : P 1 21 1 #CELL : 5.558 8.776 25.153 90 95.46 90 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff O(1) 4.5 0.066032 5.21368 4.43397 O(2) 4.3 0.0620116 4.89624 4.23799 O(3) 3.2 0.0436389 3.44559 3.15636 O(8) 3.4 0.0446362 3.52433 3.35536 O(17) 10.4 0.169959 13.4195 10.23 O(18) 10.7 0.16486 13.0168 10.5351 N(1) 3.1 0.0431873 3.40993 3.05681 N(16) 7.4 0.116793 9.22161 7.28321 N(1D1) 3.6 0.0485377 3.83238 3.55146 N(1E1) 3 0.0376687 2.9742 2.96233 C(1A) 2.6 0.0349832 2.76216 2.56502 C(1B) 3.4 0.0457167 3.60965 3.35428 C(1G) ? 0.035568 2.80834 . C(1D1) 3 0.0392694 3.10059 2.96073 C(1E1) 3.5 0.0463733 3.66149 3.45363 C(1') 2.9 0.0370491 2.92528 2.86295 C(1) 3.3 0.042418 3.34919 3.25758 C(4) 3.2 0.0411516 3.2492 3.15885 C(5) 4.3 0.0560594 4.42627 4.24394 C(6) 4.8 0.0752015 5.93767 4.7248 C(7) 5 0.0681749 5.38287 4.93183 C(9) 4.4 0.0562013 4.43748 4.3438 C(10) 3.7 0.0490885 3.87588 3.65091 C(11) 4.9 0.0650801 5.13852 4.83492 C(12) 5.8 0.0826636 6.52686 5.71734 C(13) 5.1 0.0753709 5.95104 5.02463 C(14) 5.5 0.0725431 5.72777 5.42746 C(15) 4.5 0.0580228 4.58129 4.44198 C(19) 3.5 0.0459126 3.62511 3.45409 C(20) 3.4 0.0452414 3.57212 3.35476 C(21) 4.5 0.0580925 4.5868 4.44191 C(22) 5.5 0.0720799 5.6912 5.42792 C(23) 5.6 0.0737394 5.82223 5.52626 C(24) 5.6 0.0744723 5.8801 5.52553 C(25) 4.8 0.0614525 4.8521 4.73855 #FILENAME : - #DATABLCK : 2004354 Biso instead of Uiso #SPCGRP : P 1 21 1 #CELL : 6.5104 12.812 13.480 90 98.09 90 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff O1 8.1 0.103269 8.15377 7.99673 O2 5.1 0.0641378 5.06412 5.03586 O3 9.3 0.117778 9.29937 9.18222 O4 4.9 0.0621834 4.90981 4.83782 O5 6.8 0.086425 6.82384 6.71358 O6 8 0.10084 7.96197 7.89916 C1 6.1 0.0771844 6.09424 6.02282 C2 6.5 0.0820368 6.47737 6.41796 C3 4.8 0.0612902 4.83928 4.73871 C4 4.5 0.057055 4.50488 4.44295 C5 4.3 0.0543344 4.29008 4.24567 C6 5.4 0.0686524 5.42058 5.33135 C7 5.1 0.0648486 5.12024 5.03515 C8 5.7 0.0724619 5.72136 5.62754 C9 5.6 0.0703527 5.55483 5.52965 C10 4.8 0.0605052 4.7773 4.73949 C11 5.7 0.0721742 5.69865 5.62783 C12 7.2 0.0913076 7.20936 7.10869 C13 8.2 0.102512 8.09403 8.09749 C14 6.1 0.0770002 6.07969 6.023 C15 6.7 0.0852912 6.73432 6.61471 C16 6.7 0.0843729 6.66182 6.61563 C17 7.5 0.094867 7.4904 7.40513 C18 5.7 0.0721705 5.69835 5.62783 C19 5.9 0.0752243 5.93947 5.82478 C20 8.4 0.105642 8.34119 8.29436 C21 8.4 0.106476 8.407 8.29352 C22 11.1 0.141797 11.1959 10.9582 #FILENAME : - #DATABLCK : 2004427 Biso instead of Uiso #SPCGRP : P 1 #CELL : 8.818 10.8750 12.023 110.450 92.53 107.300 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff C(1) 4.5 0.0570262 4.50261 4.44297 C(2) 4.5 0.0573977 4.53194 4.4426 C(3) 5.5 0.0701884 5.54185 5.42981 C(4) 7.2 0.0904715 7.14335 7.10953 C(5) 6.2 0.0783736 6.18813 6.12163 C(6) 5.4 0.0681098 5.37774 5.33189 C(7) 4.4 0.056191 4.43666 4.34381 C(8) 4.5 0.0572791 4.52258 4.44272 C(9) 4.5 0.056598 4.4688 4.4434 C(10) 5.8 0.0738756 5.83298 5.72612 C(11) 6.4 0.0812821 6.41778 6.31872 C(12) 5.8 0.0738666 5.83228 5.72613 C(13) 5.1 0.0643314 5.0794 5.03567 C(14) 4.4 0.0553756 4.37228 4.34462 C(15) 4.8 0.0604044 4.76934 4.7396 C(16) 5.4 0.0687222 5.42609 5.33128 C(17) 5.4 0.0690746 5.45391 5.33093 C(18) 8 0.101566 8.01936 7.89843 C(19) 6.2 0.0790407 6.2408 6.12096 N(20) 5.3 0.0663862 5.24164 5.23361 C(21) 6 0.0755333 5.96387 5.92447 C(22) 6.7 0.0848301 6.69792 6.61517 C(23) ? 0.0741315 5.85319 . C(24) 6 0.0755411 5.96448 5.92446 C(25) 7.8 0.0994836 7.85491 7.70052 C(26) ? 0.0805599 6.36075 . C(27) 7.2 0.0913392 7.21185 7.10866 C(28) 6.8 0.0865476 6.83353 6.71345 C(29) 5.1 0.0639747 5.05124 5.03603 N(30) 5 0.0644557 5.08922 4.93554 C(31) 6.7 0.0847821 6.69413 6.61522 C(32) 8 0.10066 7.94776 7.89934 O(33) 7.4 0.0937322 7.4008 7.30627 C(34) 7.3 0.0922739 7.28565 7.20773 C(35) 7.6 0.0956405 7.55147 7.50436 O(36) 6.5 0.0819111 6.46744 6.41809 C(37) 6.9 0.0871171 6.87849 6.81288 C(38) 6.7 0.0843316 6.65856 6.61567 Cl(40) ? 0.100098 7.90346 . O(41) 22.9 0.291049 22.9803 22.609 O(42) 12.9 0.163155 12.8822 12.7368 O(43) 16 0.202759 16.0092 15.7972 O(44) 12.8 0.162016 12.7922 12.638 Cl(50) 6.6 0.08388 6.6229 6.51612 O(51) 10.6 0.133352 10.5291 10.4666 O(52) 11.1 0.139889 11.0452 10.9601 O(53) 22.8 0.289248 22.8381 22.5108 O(54) 18.6 0.236397 18.6652 18.3636 C(60) 8.2 0.103389 8.16325 8.09661 C(61) 11.9 0.150749 11.9027 11.7493 C(62) 9.2 0.116859 9.22681 9.08314 C(63) 9.8 0.124247 9.81012 9.67575 C(64) 7.3 0.0923937 7.29511 7.20761 C(65) 11.3 0.143266 11.3118 11.1567 C(66) 13.3 0.168505 13.3046 13.1315 #FILENAME : - #DATABLCK : 2004531 Biso instead of Uiso #SPCGRP : P 1 21 1 #CELL : 8.4670 5.5260 35.792 90.00 90.290 90.00 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff C1 4.6 0.0580757 4.58548 4.54192 C2 5 0.0634422 5.00919 4.93656 C3 5 0.0629334 4.96903 4.93707 C4 4.3 0.0539265 4.25786 4.24607 C5 4.5 0.0570347 4.50328 4.44297 C6 4.7 0.0592684 4.67964 4.64073 O7 4.8 0.0611886 4.83126 4.73881 C8 4.2 0.0537454 4.24357 4.14625 O9 5.5 0.0694109 5.48047 5.43059 C10 4 0.0501824 3.96224 3.94982 C11 4.5 0.0565054 4.46149 4.44349 C12 4.7 0.0593125 4.68313 4.64069 C13 4.5 0.0565447 4.46459 4.44346 C14 5.2 0.0652954 5.15552 5.1347 C15 4.7 0.0596263 4.7079 4.64037 C16 5 0.0628145 4.95963 4.93719 C17 4.7 0.0598285 4.72387 4.64017 O18 5.1 0.0639832 5.05191 5.03602 C19 4.8 0.0602788 4.75942 4.73972 C20 4.4 0.055801 4.40587 4.3442 C21 5 0.0630735 4.98008 4.93693 C22 4.8 0.0602384 4.75623 4.73976 C23 4.1 0.0524255 4.13935 4.04757 C24 4.9 0.061626 4.8658 4.83837 C25 4.9 0.0625705 4.94037 4.83743 C26 4.8 0.0608707 4.80616 4.73913 C27 4.9 0.0620107 4.89617 4.83799 C28 5.2 0.065827 5.19749 5.13417 C29 5.6 0.0709611 5.60286 5.52904 C30 6.4 0.0803419 6.34354 6.31966 C31 7.7 0.0968847 7.64971 7.60312 C32 5.5 0.0695243 5.48942 5.43048 O33 7 0.0884006 6.97983 6.9116 O34 8.6 0.108497 8.56655 8.4915 C35 7.9 0.099959 7.89245 7.80004 C36 9.9 0.125471 9.90683 9.77453 C37 10.3 0.130167 10.2776 10.1698 C38 12.5 0.158403 12.507 12.3416 C39 14.3 0.18153 14.333 14.1185 C40 13 0.164873 13.0179 12.8351 C41 15.8 0.200151 15.8033 15.5998 C42 15.1 0.190985 15.0796 14.909 #FILENAME : - #DATABLCK : 2004782 Biso instead of Uiso #SPCGRP : P 1 21 1 #CELL : 11.494 6.263 12.479 90.00 111.01 90.00 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff O1 5.3 0.0678492 5.35716 5.23215 O2 5.1 0.0649676 5.12964 5.03503 N1 4.1 0.0523023 4.12963 4.0477 N2 3.4 0.0428302 3.38173 3.35717 C1 5.1 0.0637412 5.0328 5.03626 C2 5.5 0.0704409 5.56179 5.42956 C3 5.1 0.0638661 5.04267 5.03613 C4 4.9 0.0614029 4.84818 4.8386 C5 4 0.0501929 3.96307 3.94981 C6 4.2 0.0538729 4.25363 4.14613 C7 3.9 0.0482498 3.80965 3.85175 C8 3.2 0.0403431 3.18536 3.15966 C9 4.1 0.051439 4.06146 4.04856 C10 5.1 0.0648704 5.12196 5.03513 C11 4.9 0.0618926 4.88685 4.83811 C12 4.5 0.0571842 4.51509 4.44282 C13 3.9 0.0495166 3.90967 3.85048 C14 3.7 0.0466836 3.68599 3.65332 C15 4 0.0504341 3.98212 3.94957 C16 5 0.0638444 5.04095 4.93616 C17 6.8 0.0869143 6.86248 6.71309 C18 7.4 0.0945233 7.46326 7.30548 C19 5.5 0.0699076 5.51968 5.43009 C20 4.6 0.0579282 4.57383 4.54207 #FILENAME : - #DATABLCK : 2004836 Biso instead of Uiso #SPCGRP : P b c a #CELL : 8.752 27.084 17.973 90.00 90.00 90.00 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff Cl 4.93 0.0624667 4.93217 4.86753 Ow1 6.6 0.083 6.55342 6.517 Ow2 5.9 0.0746667 5.89544 5.82533 O1 4.6 0.0583333 4.60582 4.54167 O2 4.9 0.0616667 4.869 4.83833 N 3.4 0.043 3.39514 3.357 C1 11.7 0.149 11.7646 11.551 C2 7.3 0.092 7.26403 7.208 C3 5.7 0.072 5.68489 5.628 C4 4.3 0.054 4.26367 4.246 C5 4.2 0.0536667 4.23735 4.14633 C6 3.8 0.0476667 3.76361 3.75233 C7 4.8 0.0606667 4.79005 4.73933 C8 4.9 0.0623333 4.92164 4.83767 C9 4.8 0.0613333 4.84269 4.73867 C10 3.5 0.044 3.4741 3.456 C11 4.3 0.055 4.34263 4.245 C12 4.7 0.059 4.65845 4.641 C13 6.8 0.086 6.79029 6.714 C14 11.7 0.146667 11.5803 11.5533 C15 16.6 0.209 16.502 16.391 C16 5 0.063 4.97428 4.937 #FILENAME : - #DATABLCK : 2005572 Biso instead of Uiso #SPCGRP : P 1 21/n 1 #CELL : 7.755 15.352 13.508 90 95.73 90 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff O1 6.7 0.0845623 6.67677 6.61544 N1 4.5 0.0570088 4.50123 4.44299 C1 3.3 0.0421452 3.32765 3.25785 C2 3.2 0.0406701 3.21118 3.15933 C3 3.3 0.0418348 3.30314 3.25817 O4A 4.9 0.0623551 4.92336 4.83764 O4B 5.7 0.0721329 5.69539 5.62787 N4 3.9 0.0499564 3.9444 3.85004 C4 3.2 0.0403167 3.18328 3.15968 C5 3.7 0.0472499 3.7307 3.65275 C6 3.8 0.0484924 3.8288 3.75151 C7 3.4 0.0428852 3.38608 3.35711 O8 4.8 0.0607386 4.79573 4.73926 C8 3.5 0.0445821 3.52006 3.45542 O9A 9.3 0.117961 9.31383 9.18204 O9B 6 0.0765908 6.04736 5.92341 N9 4.6 0.0580509 4.58351 4.54195 C9 3.6 0.0454242 3.58655 3.55458 C10 3.5 0.0448348 3.54001 3.45517 O11A 6.2 0.0780314 6.16111 6.12197 O11B 6.3 0.0801367 6.32734 6.21986 N11 4.6 0.0577578 4.56037 4.54224 C11 3.6 0.0453832 3.58332 3.55462 C12 3.5 0.0451614 3.5658 3.45484 O13 4.7 0.0591293 4.66866 4.64087 C13 4.1 0.0516162 4.07545 4.04838 C14 7.1 0.0899944 7.10567 7.01001 #FILENAME : - #DATABLCK : 2006511 Biso instead of Uiso; problems with orthogonalisation? #SPCGRP : C 1 2/c 1 #CELL : 17.427 10.021 28.639 90 106.710 90 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff W 3.565 0.0451661 3.56617 3.51983 Cu 4.51 0.0571076 4.50904 4.45289 S 5.5 0.0696131 5.49643 5.43039 S1 5.07 0.0644667 5.09009 5.00553 S2 4.94 0.0626713 4.94833 4.87733 P 3.74 0.0474147 3.74371 3.69259 N1 6.6 0.0830345 6.55614 6.51697 N2 7.1 0.0908511 7.17332 7.00915 C1 5 0.0638708 5.04304 4.93613 C2 7.7 0.0969916 7.65815 7.60301 C3 9 0.114016 9.00233 8.88598 C4 9.1 0.115556 9.12396 8.98444 C11 3.9 0.0487161 3.84647 3.85128 C12 4.4 0.0559772 4.41978 4.34402 C13 5.5 0.0691185 5.45738 5.43088 C14 6.3 0.0796505 6.28895 6.22035 C15 6.1 0.077855 6.14718 6.02215 C16 5.1 0.0648497 5.12033 5.03515 C21 3.8 0.048461 3.82633 3.75154 C22 6.5 0.082703 6.52997 6.4173 C23 8.2 0.103491 8.17136 8.09651 C24 6.9 0.087914 6.94141 6.81209 C25 7 0.0883528 6.97606 6.91165 C26 5.8 0.073625 5.8132 5.72638 C31 3.7 0.0472072 3.72733 3.65279 C32 4.8 0.060027 4.73955 4.73997 C33 6.4 0.0802366 6.33523 6.31976 C34 7.5 0.0947773 7.48332 7.40522 C35 7.4 0.0940877 7.42887 7.30591 C36 6 0.0754592 5.95802 5.92454 #FILENAME : - #DATABLCK : 2011176 Biso instead of Uiso #SPCGRP : P 1 21/n 1 #CELL : 11.226 17.836 12.932 90 111.320 90 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff Ni 2.89 0.036551 2.88595 2.85345 P1 2.92 0.0369707 2.91909 2.88303 P2 2.9 0.0366646 2.89492 2.86334 C1 3.1 0.0386807 3.05411 3.06132 C11 3.4 0.042888 3.3863 3.35711 C12 5.9 0.0750032 5.92201 5.825 C13 7.3 0.0924345 7.29834 7.20757 C14 6.6 0.083577 6.59898 6.51642 C15 5.6 0.0705313 5.56893 5.52947 C16 4.5 0.0565032 4.46132 4.4435 C21 3.2 0.0407939 3.22096 3.15921 C22 4.5 0.056846 4.48838 4.44315 C23 6 0.0759255 5.99484 5.92407 C24 6.6 0.0839544 6.62877 6.51605 C25 7.2 0.091586 7.23134 7.10841 C26 5.2 0.066142 5.22236 5.13386 C31 3.2 0.0401048 3.16655 3.1599 C32 4.3 0.0538948 4.25536 4.24611 C33 5.7 0.0717551 5.66556 5.62824 C34 6.1 0.0778254 6.14485 6.02217 C35 5.7 0.0726034 5.73253 5.6274 C36 4.4 0.0556512 4.39404 4.34435 C41 3.1 0.0390968 3.08696 3.0609 C42 4.1 0.0514515 4.06245 4.04855 C43 5.5 0.069518 5.48892 5.43048 C44 6.4 0.0806753 6.36987 6.31932 C45 6.6 0.083402 6.58516 6.5166 C46 4.7 0.0593762 4.68816 4.64062 Cl 4.1 0.0521929 4.12098 4.04781 O1 4.8 0.0611488 4.82811 4.73885 O2 7.1 0.0900569 7.11061 7.00994 O3 7.5 0.0953584 7.5292 7.40464 O4 6.9 0.0872812 6.89144 6.81272 #FILENAME : - #DATABLCK : 2201604 Negative Uiso; Bad refinement? #SPCGRP : P -1 #CELL : 13.0046 14.0710 7.9235 92.79 96.95 71.850 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff O1 0.0628 0.0628959 4.96606 -9.58864e-05 O2 0.0594 0.0596658 4.71103 -0.000265847 O3 0.0611 0.061685 4.87046 -0.000585041 O4 0.0676 0.0676883 5.34446 -8.83306e-05 O5 0.159 0.159095 12.5617 -9.53698e-05 N1 0.077 0.0774591 6.11592 -0.000459093 N2 0.156 0.156471 12.3545 -0.000471004 C1 0.0637 0.0635402 5.01693 0.000159816 C2 0.08 0.0807714 6.37745 -0.00077136 C3 0.101 0.100604 7.94334 0.000396444 C4 0.116 0.116082 9.16549 -8.22559e-05 C5 0.122 0.122583 9.67873 -0.00058261 C6 0.094 0.0934881 7.38153 0.00051188 C7 0.0592 0.05936 4.68688 -0.00016004 C8 0.07 0.0703537 5.5549 -0.000353692 C9 0.089 0.088551 6.9917 0.000449044 C10 0.098 0.0980264 7.73985 -2.63949e-05 C11 0.107 0.107045 8.45192 -4.47593e-05 C12 0.083 0.0833444 6.58061 -0.000344364 C13 0.0538 0.0538215 4.24957 -2.14623e-05 C14 0.075 0.0747864 5.9049 0.000213622 C15 0.099 0.0994125 7.8493 -0.000412512 C16 0.096 0.0965774 7.62545 -0.000577425 C17 0.094 0.0940017 7.42208 -1.71541e-06 C18 0.075 0.0746367 5.89308 0.000363303 C19 0.119 0.118804 9.38038 0.000196155 C20 0.146 0.145989 11.5269 1.0669e-05 C21 0.186 0.18635 14.7136 -0.000350416 C22 0.252 -1.10958 -87.6089 1.36158 C23 0.179 0.180816 14.2766 -0.00181579 C24 0.269 0.268135 21.1711 0.000865204 C25 0.219 0.219554 17.3353 -0.000553881 B1 0.058 0.0580198 4.58106 -1.98282e-05 B2 0.0531 0.0533523 4.21253 -0.000252258 B3 0.0518 0.0516985 4.08195 0.000101496 #FILENAME : - #DATABLCK : 4114580 Negative Uiso; Bad refinement? #SPCGRP : C 1 c 1 #CELL : 36.389 13.313 12.704 90 104.98 90 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff Co(1) 0.0259 0.0258513 2.04114 4.87133e-05 Co(2) 0.0287 0.0287028 2.26628 -2.77274e-06 Cl(1) 0.0458 0.0459019 3.62427 -0.000101857 Cl(2) 0.0627 0.0627131 4.95163 -1.30672e-05 Cl(3) 0.0536 0.0535627 4.22914 3.72916e-05 Cl(4) 0.0427 0.0427121 3.37241 -1.20884e-05 Cl(5) 0.0562 0.0561072 4.43005 9.27896e-05 Cl(6) 0.0701 0.0701564 5.53932 -5.63604e-05 O(1) 0.103 0.102678 8.10716 0.000321606 O(2) 0.064 0.0644747 5.09072 -0.000474706 O(3) 0.089 0.0889434 7.02269 5.65995e-05 O(4) 0.092 0.0915486 7.22839 0.000451386 O(5) 0.243 0.245752 19.4038 -0.0027519 O(6) 0.116 0.115588 9.12647 0.000411959 O(7) 0.135 0.135312 10.6838 -0.00031227 O(8) 0.178 -2.93053 -231.385 3.10853 O(9) 0.105 0.104677 8.26496 0.000323111 O(10) 0.097 0.0966181 7.62866 0.000381922 O(11) 0.126 0.127992 10.1059 -0.00199219 O(12) 0.082 0.0814453 6.43066 0.00055468 O(13) 0.052 0.0519199 4.09943 8.00927e-05 O(14) 0.079 0.0786272 6.20815 0.00037282 O(15) 0.097 0.0968904 7.65016 0.000109555 O(16) 0.075 0.0744841 5.88103 0.000515858 O(17) 0.09 0.0899481 7.10202 5.18604e-05 O(18) 0.096 0.0956984 7.55604 0.000301634 O(19) 0.102 0.101154 7.98682 0.000845801 O(20) 0.09 0.0900831 7.11268 -8.30896e-05 O(21) 0.212 0.211727 16.7173 0.000273182 O(22) 0.198 0.203037 16.0311 -0.00503658 O(23) 0.13 0.129207 10.2018 0.000793294 O(24) 0.24 0.236969 18.7103 0.00303125 O(25) 0.106 0.106323 8.3949 -0.000322707 O(26) 0.174 0.174116 13.7476 -0.00011579 N(1) 0.049 0.0490333 3.87151 -3.33029e-05 N(2) 0.035 0.0345501 2.72797 0.000449861 N(3) 0.034 0.034259 2.70498 -0.000259016 N(4) 0.056 0.0563721 4.45096 -0.000372118 N(5) 0.03 0.0302043 2.38483 -0.000204276 N(6) 0.031 0.0311874 2.46246 -0.00018742 N(7) 0.063 0.062658 4.94728 0.000342023 N(8) 0.028 0.0276686 2.18463 0.000331355 N(9) 0.034 0.0343009 2.70829 -0.000300894 N(10) 0.059 0.0593491 4.68602 -0.000349114 N(11) 0.048 0.0475667 3.75572 0.000433299 N(12) 0.039 0.0395325 3.12136 -0.000532539 N(13) 0.034 0.0337884 2.66782 0.000211617 N(14) 0.041 0.0415278 3.2789 -0.000527802 N(15) 0.036 0.0355806 2.80933 0.000419358 N(16) 0.033 0.0335615 2.64991 -0.000561475 N(17) 0.053 0.0528282 4.17115 0.000171755 N(18) 0.033 0.032741 2.58513 0.000258976 N(19) 0.035 0.0350443 2.76698 -4.42662e-05 N(20) 0.065 0.0651542 5.14437 -0.000154236 C(1) 0.05 0.0493421 3.8959 0.000657896 C(2) 0.038 0.0377587 2.98131 0.000241297 C(3) 0.039 0.0394269 3.11302 -0.000426858 C(4) 0.042 0.0415677 3.28206 0.00043226 C(5) 0.064 0.0636902 5.02877 0.000309838 C(6) 0.046 0.0461527 3.64407 -0.000152669 C(7) 0.053 0.0533226 4.21018 -0.000322565 C(8) 0.061 0.0605407 4.7801 0.000459296 C(9) 0.046 0.0464724 3.66931 -0.000472356 C(10) 0.042 0.0418795 3.30667 0.000120481 C(11) 0.04 0.0405142 3.19887 -0.000514155 C(12) 0.045 0.0450678 3.55841 -6.77984e-05 C(13) 0.046 0.0454786 3.59085 0.000521379 C(14) 0.038 0.0380674 3.00568 -6.73872e-05 C(15) 0.05 0.0497558 3.92856 0.000244174 C(16) 0.044 0.0433693 3.4243 0.000630719 C(17) 0.085 0.0851311 6.72168 -0.000131115 C(18) 0.048 0.0483318 3.81612 -0.000331768 C(19) 0.059 0.0588819 4.64913 0.000118131 C(20) 0.042 0.0415248 3.27867 0.000475215 C(21) 0.029 0.0294895 2.3284 -0.000489506 C(22) 0.037 0.0370486 2.92524 -4.86312e-05 C(23) 0.056 0.0563275 4.44744 -0.000327481 C(24) 0.037 0.0370117 2.92232 -1.16706e-05 C(25) 0.047 0.0470587 3.71561 -5.86961e-05 C(26) 0.039 0.0389617 3.07629 3.82936e-05 C(27) 0.033 0.0329014 2.59779 9.85545e-05 C(28) 0.04 0.0404011 3.18994 -0.000401093 C(29) 0.046 0.0459578 3.62868 4.22474e-05 C(30) 0.044 0.0440154 3.47531 -1.53692e-05 C(31) 0.047 0.0470756 3.71694 -7.55912e-05 C(32) 0.047 0.0470939 3.71839 -9.3936e-05 C(33) 0.039 0.0387579 3.0602 0.00024212 C(34) 0.038 0.0380208 3.002 -2.07729e-05 C(35) 0.053 0.0543288 4.28963 -0.00132875 C(36) 0.05 0.0499617 3.94482 3.82936e-05 #FILENAME : - #DATABLCK : 4115051 Negative Uiso; Bad refinement? #SPCGRP : C 1 2/c 1 #CELL : 13.531 15.432 14.2106 90 95.896 90 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff F(1) 0.0198 0.0197746 1.56134 2.53504e-05 F(2) 0.0196 0.0196691 1.55301 -6.91144e-05 N(1) 0.0287 0.0289157 2.28309 -0.000215678 N(2) 0.0245 0.0245518 1.93854 -5.18497e-05 C(1) 0.0139 0.0135406 1.06912 0.000359397 C(2) 0.0144 -1.57748 -124.553 1.59188 C(3) 0.0131 0.0130417 1.02973 5.8275e-05 C(4) 0.012 0.0122003 0.963301 -0.000200348 C(5) 0.0123 -2.61766 -206.682 2.62996 C(6) 0.0142 0.0143756 1.13505 -0.000175624 C(7) 0.0242 0.0242157 1.91199 -1.56984e-05 C(8) 0.038 0.037943 2.99586 5.70218e-05 C(9) 0.0191 0.0192327 1.51855 -0.000132719 C(10) 0.0204 0.0204785 1.61692 -7.85091e-05 C(11) 0.016 0.015931 1.25786 6.89978e-05 C(12) 0.0191 0.0192294 1.51829 -0.000129352 C(13) 0.018 0.0185127 1.46171 -0.000512746 C(14) 0.014 0.0138904 1.09674 0.000109592 C(15) 0.0227 0.0227458 1.79594 -4.58158e-05 C(16) 0.013 0.0131418 1.03763 -0.0001418 C(17) 0.0147 0.0145032 1.14513 0.000196804 C(18) 0.0132 0.0130664 1.03168 0.000133579 C(19) 0.015 0.0151527 1.19641 -0.000152653 C(20) 0.019 0.0189544 1.49658 4.56216e-05 C(21) 0.017 0.0169577 1.33893 4.22552e-05 #FILENAME : - #DATABLCK : 4115055 Negative Uiso; Bad refinement? #SPCGRP : C 1 2/c 1 #CELL : 25.664 8.2817 21.057 90 144.662 90 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff F(1) 0.0232 0.0231824 1.83041 1.75588e-05 F(2) 0.022 0.0219581 1.73374 4.18696e-05 N(1) 0.0272 -47.0676 -3716.31 47.0948 N(2) 0.0262 0.0251861 1.98862 0.00101389 C(1) 0.015 0.0155217 1.22554 -0.000521695 C(2) 0.0142 0.0138259 1.09165 0.00037407 C(3) 0.0146 0.0142415 1.12446 0.000358495 C(4) 0.0136 0.0135865 1.07275 1.34594e-05 C(5) 0.0138 0.0141773 1.11939 -0.000377256 C(6) 0.0177 -22.7178 -1793.73 22.7355 C(7) 0.0146 0.0145439 1.14834 5.6093e-05 C(8) 0.0188 0.0177211 1.3992 0.0010789 C(9) 0.0216 0.0217477 1.71713 -0.000147684 C(10) 0.0202 -27.5877 -2178.23 27.6079 C(11) 0.019 0.0205388 1.62168 -0.00153878 C(12) 0.0161 0.0157899 1.24672 0.000310055 C(13) 0.0148 0.0149345 1.17918 -0.000134512 C(14) 0.0156 0.01584 1.25067 -0.000239972 C(16) 0.0158 0.0156134 1.23278 0.000186613 C(17) 0.0194 0.0184426 1.45617 0.000957386 C(18) 0.019 -25.9647 -2050.09 25.9837 #FILENAME : - #DATABLCK : 4115066 Negative Uiso; Bad refinement? #SPCGRP : P 1 n 1 #CELL : 10.364 9.406 15.504 90 107.08 90 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff N(1) 0.034 0.0342028 2.70054 -0.000202785 N(2) 0.0329 0.032951 2.60171 -5.10311e-05 N(3) 0.0418 0.0418908 3.30756 -9.07899e-05 N(4) 0.041 0.0409096 3.23009 9.04462e-05 C(1) 0.0206 0.0203931 1.61017 0.000206903 C(2) 0.0198 0.0194484 1.53558 0.000351637 C(3) 0.0189 -1.47953 -116.819 1.49843 C(4) 0.0182 0.0177728 1.40329 0.000427176 C(5) 0.0184 0.0182347 1.43976 0.000165269 C(6) 0.0193 -1.4791 -116.785 1.4984 C(7) 0.0252 0.0253328 2.0002 -0.000132797 C(8) 0.023 0.0233999 1.84758 -0.00039993 C(9) 0.022 0.0222486 1.75668 -0.000248579 C(10) 0.0235 0.0239212 1.88875 -0.00042124 C(11) 0.0191 0.0193939 1.53128 -0.000293936 C(12) 0.018 0.0178472 1.40915 0.000152849 C(13) 0.0193 0.0193948 1.53135 -9.47745e-05 C(14) 0.0185 0.0182034 1.43729 0.000296557 C(15) 0.019 0.0193948 1.53135 -0.000394775 C(16) 0.0199 0.0202771 1.60101 -0.00037708 C(17) 0.0232 0.023161 1.82872 3.89957e-05 C(18) 0.0316 0.0312997 2.47133 0.000300291 C(19) 0.0245 0.0244391 1.92963 6.09286e-05 C(20) 0.0225 0.0227018 1.79246 -0.000201794 C(21) 0.0274 0.0273438 2.15898 5.6175e-05 C(22) 0.0213 0.0214969 1.69732 -0.000196854 C(23) 0.0232 0.0227001 1.79233 0.000499883 C(24) 0.0296 0.0294171 2.32268 0.000182926 C(25) 0.0222 0.021979 1.73539 0.000220978 C(26) 0.0241 0.0241695 1.90835 -6.95153e-05 C(27) 0.0281 0.0278439 2.19846 0.000256146 C(28) 0.0229 0.0232571 1.83631 -0.00035709 C(29) 0.0251 0.0248821 1.96461 0.000217902 C(30) 0.022 0.0219084 1.72982 9.1588e-05 C(31) 0.0243 0.0242078 1.91137 9.22404e-05 C(32) 0.0205 0.0203 1.60283 0.000199962 C(33) 0.024 0.0238225 1.88095 0.000177485 C(34) 0.0244 0.0242434 1.91418 0.000156577 C(35) 0.0229 0.0229407 1.81133 -4.072e-05 C(36) 0.0228 0.022638 1.78743 0.000161983 C(37) 0.0211 0.0211677 1.67134 -6.77473e-05 C(38) 0.0265 0.0266363 2.10312 -0.000136339 C(39) 0.0329 0.0327367 2.58479 0.000163259 C(40) 0.0309 0.030798 2.43171 0.000101998 #FILENAME : - #DATABLCK : 4320747 Biso instead of Uiso #SPCGRP : P 1 2/n 1 #CELL : 8.428 9.605 15.096 90. 104.35 90. #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff Cu 3.92 0.0496072 3.91683 3.87039 Cl 5.08 0.0643338 5.07959 5.01567 S(1) 4.71 0.0596868 4.71268 4.65031 S(2) 4.09 0.051875 4.09589 4.03812 O(1) 11.7 0.147647 11.6577 11.5524 O(2) 14.2 0.179247 14.1527 14.0208 O(3) 12 0.153551 12.1239 11.8464 O(4) 16.1 0.204606 16.155 15.8954 N(1) 4.7 0.0596083 4.70648 4.64039 N(2) 4.01 0.0506607 4.00001 3.95934 C(1) 4 0.0507388 4.00617 3.94926 C(2) 7.2 0.0910903 7.1922 7.10891 C(3) 7.9 0.0997822 7.87849 7.80022 C(4) 3.69 0.04672 3.68887 3.64328 C(5) 5.7 0.07274 5.74332 5.62726 C(6) 5.9 0.0747572 5.90259 5.82524 H(1) 4.5 0.0243645 1.92374 4.47564 0.14(1) ? 0.0506667 4.00048 . H(8) 4.2 0.0460469 3.63572 4.15395 0.1520 ? 0.0333333 2.63189 . #FILENAME : - #DATABLCK : 4321814 Biso instead of Uiso #SPCGRP : C m c 21 #CELL : 11.889 33.380 9.012 90 90 90 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff CU1 2.5 0.0316667 2.5003 2.46833 CU2 2.9 0.0366667 2.89508 2.86333 CU3 3 0.038 3.00036 2.962 CU4 2.9 0.0366667 2.89508 2.86333 CU5 2.91 0.037 2.9214 2.873 CU6 3.8 0.0482667 3.81098 3.75173 N21 3.3 0.041 3.23723 3.259 N31 2.8 0.0356667 2.81613 2.76433 N61 3.2 0.0403333 3.18459 3.15967 C21 9 0.113333 8.94844 8.88667 C22 9 0.11 8.68525 8.89 C23 5.4 0.0683333 5.39538 5.33167 C31 9 0.113333 8.94844 8.88667 C32 8 0.1 7.89568 7.9 C33 5 0.0636667 5.02692 4.93633 C61 10 0.130333 10.2907 9.86967 C62 9 0.11 8.68525 8.89 C63 10 0.123333 9.73801 9.87667 #FILENAME : - #DATABLCK : 4323429 Biso instead of Uiso #SPCGRP : P 1 2/c 1 #CELL : 13.372 9.198 16.872 90 93.93 90 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff Zn 3.85 0.0487409 3.84842 3.80126 S(1) 4.2 0.0531509 4.19663 4.14685 S(2) 4.81 0.060901 4.80855 4.7491 N(1) 7.5 0.0954061 7.53296 7.40459 N(2) 9.1 0.115668 9.13279 8.98433 N(3) 4 0.0513102 4.05129 3.94869 N(4) 4 0.0512199 4.04416 3.94878 C(1) 3.8 0.0482658 3.81092 3.75173 C(2) 4.2 0.0534573 4.22082 4.14654 C(3) 5 0.0630907 4.98144 4.93691 C(4) 5.8 0.0731797 5.77803 5.72682 C(12) 5.1 0.064069 5.05868 5.03593 C(13) 5.5 0.0695986 5.49529 5.4304 C(14) 4.9 0.0624153 4.92811 4.83758 C(15) 5.8 0.0728891 5.75509 5.72711 C(16) 5.3 0.0667988 5.27423 5.2332 C(17) 7.3 0.092949 7.33896 7.20705 C(22) 5.3 0.0673052 5.3142 5.23269 C(23) 6.5 0.0826256 6.52386 6.41737 C(24) 5.5 0.0695571 5.49201 5.43044 C(25) 5.1 0.0646379 5.1036 5.03536 C(26) 4.5 0.0570353 4.50333 4.44296 C(27) 9.7 0.122919 9.70531 9.57708 #FILENAME : - #DATABLCK : 8101564 Biso instead of Uiso #SPCGRP : C 1 2/c 1 #CELL : 22.598 11.626 18.539 90.00 116.37 90.00 #@ label Uiso(CIF) Ueq(comp) Beq(comp) diff Au1 6.99 0.0885192 6.9892 6.90148 P1 6.3 0.0796392 6.28806 6.22036 N1 6.9 0.087013 6.87027 6.81299 N2 8 0.0978322 7.72452 7.90217 C3 11 0.138075 10.902 10.8619 C4 12 0.150121 11.8531 11.8499 C5 11 0.136648 10.7893 10.8634 C6 11 0.131269 10.3646 10.8687 C7 8 0.097724 7.71598 7.90228 C11 6.5 0.08065 6.36787 6.41935 C12 7 0.0935714 7.3881 6.90643 C13 9 0.117368 9.26704 8.88263 C14 9 0.116137 9.16984 8.88386 C15 9 0.11977 9.45664 8.88023 C16 8 0.102448 8.08901 7.89755 C17 7 0.09065 7.15744 6.90935 C18 9 0.117668 9.29066 8.88233 C19 9 0.111768 8.82488 8.88823 C20 11 0.140785 11.1159 10.8592 C21 8 0.0974767 7.69645 7.90252 C22 7 0.0863019 6.81412 6.9137 C23 7.3 0.0904854 7.14444 7.20951 Cl1 9.8 0.124393 9.82169 9.67561