From wojdyr at gmail.com Mon Mar 2 11:57:37 2020 From: wojdyr at gmail.com (Marcin Wojdyr) Date: Mon, 2 Mar 2020 10:57:37 +0100 Subject: [Cod-bugs] _atom_site_disorder_group Message-ID: Hello, last week I exchanged a few emails with Daniel Kratzert about handling _atom_site_disorder_group. Normally, the value is an integer, but it has type 'char' in the dictionary. We checked non-numeric values in COD. The full list is attached. Daniel thought that maybe SHELXL used letters (A, B) for _atom_site_disorder_group for a short time in 1993, but G. Sheldrick didn't remember it. Anyway, half of the cases with non-integer disorder group seems to be a mistake. Often a character is added to the dot (.. or \. or ?. or ...). In 2007289 it's repeated type_symbol. In 2005194 it's occupancy? For our use, we decided to just ignore all non-integer disorder groups, as they are rare and unreliable. I don't know what COD should do with it, but perhaps this list will be useful to you. Best wishes, Marcin -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- cif/1/10/06/1100679.cif:.. cif/1/10/06/1100680.cif:.. cif/1/10/06/1100689.cif:.. cif/1/51/63/1516392.cif:.. cif/1/54/76/1547641.cif:.. cif/1/55/60/1556018.cif:.. cif/1/55/64/1556489.cif:P cif/2/00/20/2002080.cif:A cif/2/00/30/2003031.cif:A cif/2/00/34/2003400.cif:A cif/2/00/34/2003400.cif:B cif/2/00/37/2003714.cif:A cif/2/00/37/2003714.cif:B cif/2/00/42/2004220.cif:A cif/2/00/51/2005194.cif:0.42(2) cif/2/00/51/2005194.cif:0.58(2) cif/2/00/59/2005976.cif:.. cif/2/00/61/2006104.cif:A cif/2/00/72/2007289.cif:N cif/2/00/72/2007289.cif:Na cif/2/00/72/2007289.cif:O cif/2/00/72/2007289.cif:V cif/2/00/72/2007289.cif:W cif/2/00/74/2007423.cif:.yes cif/2/00/76/2007617.cif:P cif/2/00/76/2007617.cif:S cif/2/00/79/2007904.cif:.. cif/2/00/81/2008103.cif:a cif/2/00/81/2008103.cif:b cif/2/00/82/2008249.cif:a cif/2/00/82/2008249.cif:b cif/2/00/82/2008292.cif:A1 cif/2/00/82/2008292.cif:B2 cif/2/00/82/2008292.cif:C1 cif/2/00/98/2009831.cif:A cif/2/00/98/2009831.cif:B cif/2/01/01/2010189.cif:A cif/2/01/01/2010189.cif:B cif/2/01/03/2010343.cif:A cif/2/01/03/2010343.cif:B cif/2/01/03/2010344.cif:A cif/2/01/03/2010344.cif:B cif/2/01/08/2010840.cif:A cif/2/01/08/2010840.cif:B cif/2/01/08/2010841.cif:A cif/2/01/08/2010841.cif:B cif/2/01/08/2010842.cif:A cif/2/01/08/2010842.cif:B cif/2/01/08/2010842.cif:C cif/2/01/08/2010842.cif:D cif/2/01/08/2010843.cif:A cif/2/01/08/2010843.cif:B cif/2/01/10/2011027.cif:A cif/2/01/10/2011027.cif:B cif/2/01/15/2011539.cif:A cif/2/01/15/2011539.cif:B cif/2/01/15/2011540.cif:A cif/2/01/15/2011540.cif:B cif/2/01/15/2011545.cif:A cif/2/01/15/2011545.cif:B cif/2/01/33/2013337.cif:A cif/2/01/33/2013337.cif:B cif/2/01/33/2013337.cif:C cif/2/01/37/2013740.cif: cif/2/01/77/2017701.cif:.. cif/2/01/93/2019390.cif:.0 cif/2/01/94/2019480.cif:GR cif/2/01/94/2019480.cif:R cif/2/10/21/2102104.cif:A cif/2/10/21/2102104.cif:B cif/2/10/21/2102105.cif:A cif/2/10/21/2102105.cif:B cif/2/10/21/2102107.cif:A cif/2/10/21/2102107.cif:B cif/2/10/21/2102108.cif:A cif/2/10/21/2102108.cif:B cif/2/10/21/2102110.cif:A cif/2/10/21/2102110.cif:B cif/2/20/19/2201977.cif:.. cif/2/20/29/2202943.cif:R cif/2/21/43/2214390.cif:.Bruker cif/2/23/55/2235573.cif:2al cif/2/31/16/2311633.cif:A cif/2/31/16/2311633.cif:B cif/4/02/00/4020043.cif:A cif/4/02/00/4020043.cif:B cif/4/02/22/4022287.cif:A cif/4/02/22/4022287.cif:B cif/4/02/22/4022287.cif:C cif/4/02/22/4022287.cif:D cif/4/02/67/4026795.cif:- cif/4/03/05/4030549.cif:.. cif/4/08/12/4081210.cif:.. cif/4/08/82/4088257.cif:P cif/4/08/84/4088488.cif:\. cif/4/08/84/4088490.cif:\. cif/4/08/84/4088494.cif:\. cif/4/08/84/4088495.cif:\. cif/4/10/75/4107517.cif:.. cif/4/11/17/4111761.cif:A cif/4/11/17/4111761.cif:B cif/4/11/28/4112884.cif:.. cif/4/11/33/4113391.cif:A cif/4/11/47/4114799.cif:A cif/4/11/47/4114799.cif:B cif/4/11/55/4115595.cif:A cif/4/11/55/4115595.cif:B cif/4/11/59/4115901.cif:A cif/4/11/59/4115905.cif:.. cif/4/11/59/4115935.cif:A cif/4/11/59/4115935.cif:B cif/4/11/59/4115935.cif:C cif/4/11/59/4115935.cif:D cif/4/13/16/4131610.cif:P cif/4/30/52/4305200.cif:.. cif/4/30/52/4305201.cif:.. cif/4/30/52/4305202.cif:.. cif/4/30/52/4305203.cif:.. cif/4/30/52/4305204.cif:.. cif/4/30/52/4305205.cif:.. cif/4/30/52/4305206.cif:.. cif/4/30/52/4305207.cif:.. cif/4/30/73/4307381.cif:.. cif/4/30/73/4307382.cif:.. cif/4/30/73/4307383.cif:.. cif/4/30/73/4307384.cif:.. cif/4/30/73/4307385.cif:.. cif/4/30/73/4307386.cif:.. cif/4/30/73/4307387.cif:.. cif/4/30/73/4307388.cif:.. cif/4/31/27/4312778.cif:.. cif/4/31/27/4312780.cif:.. cif/4/31/27/4312781.cif:.. cif/4/31/99/4319995.cif:.. cif/4/32/06/4320683.cif:.. cif/4/32/06/4320687.cif:A cif/4/32/17/4321753.cif:.. cif/4/32/23/4322388.cif:.. cif/4/32/37/4323723.cif:.. cif/4/32/76/4327695.cif:.. cif/4/33/02/4330231.cif:.. cif/4/33/22/4332275.cif:.. cif/4/33/22/4332276.cif:.. cif/4/33/22/4332277.cif:.. cif/4/33/22/4332279.cif:.. cif/4/33/22/4332281.cif:.. cif/7/00/39/7003918.cif:.? cif/7/00/39/7003919.cif:.? cif/7/00/44/7004439.cif:- cif/7/01/13/7011342.cif:A cif/7/01/13/7011342.cif:B cif/7/01/40/7014043.cif:A cif/7/01/40/7014043.cif:B cif/7/01/40/7014043.cif:C cif/7/01/40/7014043.cif:D cif/7/02/35/7023551.cif:A cif/7/02/35/7023551.cif:B cif/7/02/37/7023754.cif:.. cif/7/03/17/7031710.cif:.. cif/7/03/23/7032385.cif:.. cif/7/03/42/7034203.cif: cif/7/03/73/7037378.cif:P cif/7/03/73/7037379.cif:P cif/7/04/14/7041424.cif:PA1 cif/7/04/14/7041424.cif:PA2 cif/7/05/85/7058523.cif: cif/7/10/04/7100445.cif:A cif/7/10/04/7100445.cif:B cif/7/10/04/7100445.cif:D cif/7/10/04/7100445.cif:E cif/7/10/37/7103706.cif:A cif/7/10/37/7103706.cif:B cif/7/10/37/7103706.cif:C cif/7/10/48/7104805.cif:2= cif/7/11/34/7113466.cif:2= cif/7/11/37/7113738.cif:A cif/7/11/37/7113738.cif:B cif/7/11/37/7113738.cif:C cif/7/11/40/7114008.cif:.. cif/7/11/90/7119014.cif:P cif/7/12/53/7125388.cif:.. cif/7/15/11/7151156.cif:.1 cif/7/21/98/7219860.cif:D cif/7/21/98/7219860.cif:DR cif/7/21/98/7219860.cif:R cif/7/22/49/7224994.cif:P cif/7/23/37/7233774.cif:... cif/8/10/00/8100061.cif:i cif/8/10/17/8101711.cif:A From andrius.merkys at gmail.com Tue Mar 3 12:28:57 2020 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Tue, 3 Mar 2020 12:28:57 +0200 Subject: [Cod-bugs] _atom_site_disorder_group In-Reply-To: References: Message-ID: Hi Marcin, Thanks a lot for the interesting observation. I have opened an issue in the COD's issue tracker [1] to deal with non-numeric values of '_atom_site_disorder_group'. I have looked into a bunch of such CIF files, and fixed a couple of them. It seems that sometimes the problem is incorrect use of CIF data types, and in some cases the issue is due to typographic mistakes. We'll consider implementing checks in our software. Fixes mostly will have to be done manually. Best wishes, Andrius [1] https://projects.ibt.lt/repositories/issues/537 On 2020-03-02 11:57, Marcin Wojdyr wrote: > last week I exchanged a few emails with Daniel Kratzert about handling > _atom_site_disorder_group. Normally, the value is an integer, but it > has type 'char' in the dictionary. > > We checked non-numeric values in COD. The full list is attached. > Daniel thought that maybe SHELXL used letters (A, B) for > _atom_site_disorder_group for a short time in 1993, but G. Sheldrick > didn't remember it. > Anyway, half of the cases with non-integer disorder group seems to be a mistake. > Often a character is added to the dot (.. or \. or ?. or ...). > In 2007289 it's repeated type_symbol. In 2005194 it's occupancy? > > For our use, we decided to just ignore all non-integer disorder > groups, as they are rare and unreliable. I don't know what COD should > do with it, but perhaps this list will be useful to you. -- 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 andrius.merkys at gmail.com Tue Mar 3 12:39:40 2020 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Tue, 3 Mar 2020 12:39:40 +0200 Subject: [Cod-bugs] possible incorrect CIF file In-Reply-To: References: Message-ID: Dear Jon Tischler, Sorry for the delay. As per the original paper [1], COD entry 1006141 should have H-M symbol of 'P b m n' (see Table I). However, CIF file gives H-M symbol of 'P b n m'. Could you please check the Wyckoff letter for the site with 'P b m n' symbol? Best regards, Andrius [1] https://journals.aps.org/prb/pdf/10.1103/PhysRevB.57.R3189 On 2020-02-07 01:23, Tischler, Jon wrote: > In the CIF file for 1006141, LaMnO3 > > The H-M symbol is "P b n m" (setting 62:cab) > > The sole Mn atom is shown as: > Mn1 Mn3+ 4 a 0.5 0 0 > > Note that Wyckoff = a x,y,z = 1/2, 0, 0 > > using the Bilbao crystallographic server, > > for Pbnm, (1/2, 0, 0) is Wyckoff = b > > for Pnma (default for 62) (1/2, 0, 0) --> Wyckoff = b (for both Bilbao and International Tables) > > I have no idea how the Wyckoff = a got into the CIF file. > > > Jon Tischler > Argonne National Laboratory > tischler at anl.gov > > -- 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.