From grazulis at ibt.lt Tue Mar 18 11:12:40 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Tue, 18 Mar 2025 11:12:40 +0200 Subject: [Cod-bugs] Simulated structure in COD ? In-Reply-To: <303D37DD-FD32-41C5-9B2F-4733ECB76ACA@esrf.fr> References: <303D37DD-FD32-41C5-9B2F-4733ECB76ACA@esrf.fr> Message-ID: <523719c0-0b48-4a7f-92d8-21e1733f085f@ibt.lt> On 2025-03-18 10:43, Vincent Favre-Nicolin wrote: > Dear Saulius, > > I had a question regarding some entries in the COD - I was searching > for structures with small unit cells, and if you search the COD with > the simple constraint of 1 get 18 entries, most of which come from a single article > (https://pubs.rsc.org/en/content/articlelanding/2023/sc/d3sc04406h), > e.g. https://www.crystallography.net/cod/1570688.html I tried to reproduce you search and I get slightly different counts of structures but in the essence yes, I see a similar search result [1]. > > However if I read this correctly, the article is about simulation of > structures, and not actual ones obtained from experimental data. We'll have a look. If the structures are simulated then we'll mark them as theoretical ? thanks for the notification! Unfortunately, when the CIFs are ingested from the supplementary material it is quite hard to recognise theoretical stuff, so we'll have to rely on the post-processing review. Although, I now think, modern structures without R-factors can most probably me marked as theoretical... I forward this to our team. > > So I guess this should either be in the PCOD, or just tagged as a > theoretical structure (along with all the structures from that paper) ? We would put them into TCOD, probably (PCOD is for Armel's ans his colleagues' mass-predicted structures); but, unfortunately part of theoretical structures still land in the COD, so we can only mark them as such. > > Sorry for emailing you directly, I did not find a form to send a > report/issue from the website. No problems, your e-mail reached the correct address (it would be forwarded to me anyway ;). Its the 'cod-bugs at lists.crystallography.net' address (declared, albeit as a pixel image, on the front page of the COD Wep page, at the bottom). I redirect the conversation there so that our team sees it). Regards, Saulius References: [1] Search for a small cell 'a' structures and right angles: > saulius at pterodaktilis ~/ $ date > 2025-03-18T11:03:23 EET > saulius at pterodaktilis ~/ $ codslave 'select file, doi, a, b, c, title > from data where a > 1 and a <= 2.5 and alpha = 90 and beta = 90 and > gamma = 90' -NB | wc -l > 19 > saulius at pterodaktilis ~/ $ codslave 'select file, doi, a, b, c, title > from data where a > 1 and a <= 2.5 and alpha = 90 and beta = 90 and > gamma = 90' > +---------+----------------------------+---------+---------+---------+------------------------------------------------------------------------------------------------------------------------------------------------------------------+ > | file??? | doi??????????????????????? | a?????? | b?????? | c?????? | > title | > +---------+----------------------------+---------+---------+---------+------------------------------------------------------------------------------------------------------------------------------------------------------------------+ > | 1570692 | 10.1039/d3sc04406h???????? |? 1.1547 |? 1.1547 | 1.1547 | > Net-clipping as a top-down approach for the prediction of topologies > of MOFs built from reduced-symmetry > linkers.??????????????????????????????????????????????? | > | 1570677 | 10.1039/d3sc04406h???????? |? 1.7889 |? 1.7889 | 1.7889 | > Net-clipping as a top-down approach for the prediction of topologies > of MOFs built from reduced-symmetry > linkers.??????????????????????????????????????????????? | > | 1570676 | 10.1039/d3sc04406h???????? | 2.12045 | 2.12045 | 2.45424 | > Net-clipping as a top-down approach for the prediction of topologies > of MOFs built from reduced-symmetry > linkers.??????????????????????????????????????????????? | > | 9013111 | 10.1088/0305-4608/14/5/002 |?? 2.168 |?? 3.755 | 3.416 | > On the high-pressure phase transition in beryllium metal Sample: at P > = 28.3 GPa Note: phase II | > | 1570679 | 10.1039/d3sc04406h???????? | 2.18345 | 2.18345 | 2.18345 | > Net-clipping as a top-down approach for the prediction of topologies > of MOFs built from reduced-symmetry > linkers.??????????????????????????????????????????????? | > | 1570678 | 10.1039/d3sc04406h???????? | 2.21608 | 2.21608 | 2.21608 | > Net-clipping as a top-down approach for the prediction of topologies > of MOFs built from reduced-symmetry > linkers.??????????????????????????????????????????????? | > | 1570690 | 10.1039/d3sc04406h???????? |? 2.3094 |? 2.3094 | 2.3094 | > Net-clipping as a top-down approach for the prediction of topologies > of MOFs built from reduced-symmetry > linkers.??????????????????????????????????????????????? | > | 1570691 | 10.1039/d3sc04406h???????? |? 2.3094 |? 2.3094 | 2.3094 | > Net-clipping as a top-down approach for the prediction of topologies > of MOFs built from reduced-symmetry > linkers.??????????????????????????????????????????????? | > | 1570687 | 10.1039/d3sc04406h???????? | 2.37485 | 2.37485 | 2.16458 | > Net-clipping as a top-down approach for the prediction of topologies > of MOFs built from reduced-symmetry > linkers.??????????????????????????????????????????????? | > | 1570688 | 10.1039/d3sc04406h???????? | 2.37513 | 2.37513 | 2.16441 | > Net-clipping as a top-down approach for the prediction of topologies > of MOFs built from reduced-symmetry > linkers.??????????????????????????????????????????????? | > | 1533386 | 10.1002/pssb.200301569???? |? 2.4216 |? 2.4216 | 2.4216 | > Calculated high pressure crystal structure transformations for > phosphorus | > | 1570659 | 10.1039/d3sc04406h???????? | 2.45007 | 2.45007 | 4.89666 | > Net-clipping as a top-down approach for the prediction of topologies > of MOFs built from reduced-symmetry > linkers.??????????????????????????????????????????????? | > | 9000046 | NULL?????????????????????? |?? 2.456 |?? 4.254 | 6.696 | > The problem of the graphite structure | > | 9009217 | 10.1126/science.1095932??? |?? 2.456 |?? 8.042 | 6.093 | > Post-perovskite phase transition in MgSiO3 Sample: P = 121 GPa, T = > 300 K Note: CaIrO3-type structure from ab initio calculations using > observed cell parameters | > | 1528946 | NULL?????????????????????? |?? 2.462 |?? 8.053 | 6.108 | > Phase transition in Mg Si O3 perovskite in the earth's lower mantle | > | 9017812 | NULL?????????????????????? |?? 2.466 |??? 8.13 | 6.108 | > Single-crystal structure determination of (Mg,Fe)SiO3 postperovskite > Note: P = 120 GPa | > | 9004001 | 10.2138/am.2006.2118?????? |? 2.4687 |? 8.1165 | 6.1514 | > Equation of state of CaIrO3-type MgSiO3 up to 144 GPa Sample: P = 116 > GPa, T = 300 K | > | 1511242 | NULL?????????????????????? |???? 2.5 |??? 4.34 |??? 3.35 | > Metastable structures of graphite-like boron nitride | > | 1522164 | NULL?????????????????????? |???? 2.5 |???? 2.5 |??? 3.61 | > Leitfaehigkeit und Hallkonstante. XI. Das System Co3 V - Ni3 V - Pd3 V | > +---------+----------------------------+---------+---------+---------+------------------------------------------------------------------------------------------------------------------------------------------------------------------+ -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) mobile: (+370-684)-49802, (+370-614)-36366 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrius.merkys at gmail.com Tue Mar 18 11:28:03 2025 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Tue, 18 Mar 2025 11:28:03 +0200 Subject: [Cod-bugs] Simulated structure in COD ? In-Reply-To: <523719c0-0b48-4a7f-92d8-21e1733f085f@ibt.lt> References: <303D37DD-FD32-41C5-9B2F-4733ECB76ACA@esrf.fr> <523719c0-0b48-4a7f-92d8-21e1733f085f@ibt.lt> Message-ID: <0499b675-4660-48b4-acb5-b7ca85af6de7@gmail.com> Hello, On 2025-03-18 11:12, Saulius Gra?ulis wrote: > On 2025-03-18 10:43, Vincent Favre-Nicolin wrote: >> I had a question regarding some entries in the COD - I was searching >> for structures with small unit cells, and if you search the COD with >> the simple constraint of 1> get 18 entries, most of which come from a single article >> (https://pubs.rsc.org/en/content/articlelanding/2023/sc/d3sc04406h), >> e.g. https://www.crystallography.net/cod/1570688.html This publication has caught my eye multiple times, but I never got to the bottom of it. Nevertheless COD entries from it (especially 1570654-1570692) frequently appear when searching for unrealistic molecular geometry and crystal parameters. Interestingly, the paper seems to describe both single-crystal X-ray diffraction structure solutions and the in-silico derived structures. Entries 1570205-1570207 seem to correspond to X-ray structures while the remaining must be theoretical. I will mark them as such in the COD. Thanks, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lithuania From grazulis at ibt.lt Tue Mar 18 11:57:11 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Tue, 18 Mar 2025 11:57:11 +0200 Subject: [Cod-bugs] Simulated structure in COD ? In-Reply-To: <0499b675-4660-48b4-acb5-b7ca85af6de7@gmail.com> References: <303D37DD-FD32-41C5-9B2F-4733ECB76ACA@esrf.fr> <523719c0-0b48-4a7f-92d8-21e1733f085f@ibt.lt> <0499b675-4660-48b4-acb5-b7ca85af6de7@gmail.com> Message-ID: <883ae3c0-f020-49e5-8115-2ad82eab7d21@ibt.lt> On 2025-03-18 11:28, Andrius Merkys wrote: > Interestingly, the paper seems to describe both single-crystal X-ray > diffraction structure solutions and the in-silico derived structures. > Entries 1570205-1570207 seem to correspond to X-ray structures while > the remaining must be theoretical. I will mark them as such in the COD. Thanks, Andrius, for taking care of this! Indeed, some structures from this paper have large cells and we need to be careful to not mark experimental structures as theoretical. -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) mobile: (+370-684)-49802, (+370-614)-36366 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.