[Cod-bugs] Simulated structure in COD ?
Saulius Gražulis
grazulis at ibt.lt
Tue Mar 18 11:12:40 EET 2025
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<a<2.5 (and the default 90° for angles), you
> 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 Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
mobile: (+370-684)-49802, (+370-614)-36366
--
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