[Cod-bugs] COD conversion with HighScore
Saulius Gražulis
grazulis at ibt.lt
Mon Jan 13 09:23:14 EET 2020
Dear Thomas,
I have finished a short inspection of the COD Uij problems. I attach the
file with possible large Uij reasons identified, and a summary of the
reason frequencies (files REASONS.lst and SUMMARY.txt, respectively. The
REASONS.lst file can be read as CSV with TAB (ASCII 9) characters as
column separators.
I have only inspected files with some Bij > 300. There are 40 such
files. Lowering threshold Bij > 200 would add extra 10. Lowering to 150
adds ~320 extra files (376 total), and at Bij > 100 we have 1106 total.
Thus, Bij < 100 are very common, and Bij > 150 are relatively rare.
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).
The main reasons for large Bij values, as I see them, are these:
> saulius at koala Uiso/ $ head SUMMARY.txt
> 15 Biso instead of Uiso
> 6 Uij multiplied by 1E4?
> 5 Digits missing from some Uij values?
> 4 Bij instead of Uij
> 3 Bij instead of Uij for just one atom? (???) Or refinement problems?
> 2 Two Uij values stand out. Manual data entry error? Or refinement problems?
> 2 Bij instead of Uij?
> 1 Values for one atom ('C(1)') very large. Problems with refinement?
> 1 Two Uij values stand out. Manual data entry error? Uij multiplied by 1E4?
> 1 Two Uij values stand out. Manual data entry error? (Typed "9" instead of "0"?)
I think we can reasonably fix the first four lines, which gives 15 + 6 +
5 + 4 = 30 corrected COD records. That's doable and most probably will
be correct, but very little. The rest, IMHO, starts getting dubious. In
many cases (say for "Uij multiplied by 1E4?") we should probably contact
authors to verify that my interpretation of their files is correct.
As for the bulk of the Bij>10 structures, I would say most are organics
and have naturally higher Bij values than minerals. I'll discuss this on
the COD AB, there the people have much more experience with small
molecule crystals than me.
Taking a random structure from the COD_Conv_Warnings.csv list:
> #@ CODID AtLabel Uij data name Uij Bij> 4078519 C21 _atom_site_aniso_u_11 0.17300000 13.65953249
> 4078519 C21 _atom_site_aniso_u_33 0.16900000 13.34370515
> 4078519 C17 _atom_site_aniso_u_22 0.14600000 11.52769794
> 4078519 C19 _atom_site_aniso_u_22 0.13000000 10.26438858
> #@ label Uiso(CIF) Ueq(comp) Beq(comp) Uiso-Ueq
> C21 0.115 0.114728 9.05854000 0.00027223
> C19 0.096 0.0964213 7.61312000 -0.00042125
> C65B 0.085 0.0852352 6.72990000 -0.00023515
> C17 0.0741 0.0744293 5.87670000 -0.00032931
> C16 0.0652 0.0651477 5.14386000 0.00005231
So, the largest Bij value (U11->B11 for C21) is 13.7, the largest Biso
(again, for C21) is 9.1, and the structure, although it has some mild
disorder, looks pretty normal to me. Ueqiv computed from the Uij are
consistent, within error, with the values provided in Uiso. Do you think
Bij > 10 indicates a problem here?
Sincerely yours,
Saulius
--
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio 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 --------------
#@CODID Problem Author Possible reason
1544873 some Bij>300 S.G. Reason for large Uij not clear at all.
1544907 some Bij>300 S.G. Reason for large Uij not clear at all. Similar to 1544873
2000571 some Bij>300 S.G. Uij multiplied by 1E4?
2000642 some Bij>300 S.G. Uij multiplied by 1E4?
2000721 some Bij>300 S.G. Uij multiplied by 1E4?
2002110 some Bij>300 S.G. Uij multiplied by 1E4?
2002111 some Bij>300 S.G. Uij multiplied by 1E4?
2005112 some Bij>300 S.G. Digits missing from some Uij values? Manual data entry error?
2005689 some Bij>300 S.G. Extra digits for some Uij values? Manual data entry error?
2006293 some Bij>300 S.G. Bij instead of Uij
2006294 some Bij>300 S.G. Bij instead of Uij
2006295 some Bij>300 S.G. Bij instead of Uij
2009417 some Bij>300 S.G. Biso instead of Uiso. Uij multiplied by 1E4?
2009425 some Bij>300 S.G. Uij multiplied by 1E4?
2010272 some Bij>300 S.G. Bij instead of Uij
2101928 some Bij>300 S.G. Bij instead of Uij for just one atom? (???) Or refinement problems?
2102017 some Bij>300 S.G. Two Uij values stand out. Manual data entry error? Or refinement problems?
2201604 some Bij>300 S.G. One Uij value stands out. Manual data entry error? Digits missing from some Uij values?
4061132 some Bij>300 S.G. Values for one atom ('C(1)') very large. Problems with refinement?
4114108 some Bij>300 S.G. One Uij value stands out. Problems with refinement?
4114109 some Bij>300 S.G. Two Uij values stand out. Manual data entry error? Or refinement problems?
4114580 some Bij>300 S.G. Digits missing from some Uij values?
4114581 some Bij>300 S.G. Digits missing from some Uij values?
4115051 some Bij>300 S.G. Digits missing from some Uij values?
4115055 some Bij>300 S.G. Digits missing from some Uij values?
4115066 some Bij>300 S.G. Digits missing from some Uij values?
4116019 some Bij>300 S.G. Bij instead of Uij for just one atom? (???) Or refinement problems?
4307487 some Bij>300 S.G. Bij instead of Uij for just one atom? (???) Or refinement problems?
4322175 some Bij>300 S.G. Digits missing from some Uij values? Problems with refinement?
4322875 some Bij>300 S.G. The first (U11) value on *some*, but not *all*, hydrogens seems to be converted to B instead of U (???)
9004552 some Bij>300 S.G. Some atoms seem to have Uij, some probably have Biso specified as U11. Manual data entry error?
9007611 some Bij>300 S.G. Heavy atoms seem to have Uij, hydrogens probably have Biso specified as U11. Manual data entry error?
9009485 some Bij<-200 S.G. Large negative U23 for some atoms. Problems with refinement?
9013813 some Bij>300 S.G. Two Uij values stand out. Manual data entry error? (Typed "9" instead of "0"?)
9013821 some Bij>300 S.G. One Uij value stands out. Manual data entry error?
9014030 some Bij>300 S.G. Two Uij values stand out. Manual data entry error?
9014636 some Bij>300 S.G. One Uij value stands out. Manual data entry error? Or refinement problems?
9014842 some Bij>300 S.G. Three Uij values stand out. Manual data entry error? Uij multiplied by 1E4?
9014997 some Bij>300 S.G. Bij instead of Uij?
9016254 some Bij>300 S.G. Two Uij values stand out. Manual data entry error? Uij multiplied by 1E4?
9016691 some Bij>300 S.G. Bij instead of Uij?
2001154 Uiso-Ueq>1 S.G. Biso instead of Uiso
2001156 Uiso-Ueq>1 S.G. Biso instead of Uiso
2003303 Uiso-Ueq>1 S.G. Biso instead of Uiso
2003596 Uiso-Ueq>1 S.G. Biso instead of Uiso
2004328 Uiso-Ueq>1 S.G. Biso instead of Uiso; bad orthogonalisation?
2004354 Uiso-Ueq>1 S.G. Biso instead of Uiso
2004427 Uiso-Ueq>1 S.G. Biso instead of Uiso
2004531 Uiso-Ueq>1 S.G. Biso instead of Uiso
2004782 Uiso-Ueq>1 S.G. Biso instead of Uiso
2004836 Uiso-Ueq>1 S.G. Biso instead of Uiso
2005572 Uiso-Ueq>1 S.G. Biso instead of Uiso
2006511 Uiso-Ueq>1 S.G. Biso instead of Uiso; problems with orthogonalisation?
2011176 Uiso-Ueq>1 S.G. Biso instead of Uiso
4320747 Uiso-Ueq>1 S.G. Biso instead of Uiso
4321814 Uiso-Ueq>1 S.G. Biso instead of Uiso
4323429 Uiso-Ueq>1 S.G. Biso instead of Uiso
8101564 Uiso-Ueq>1 S.G. Biso instead of Uiso
-------------- next part --------------
15 Biso instead of Uiso
6 Uij multiplied by 1E4?
5 Digits missing from some Uij values?
4 Bij instead of Uij
3 Bij instead of Uij for just one atom? (???) Or refinement problems?
2 Two Uij values stand out. Manual data entry error? Or refinement problems?
2 Bij instead of Uij?
1 Values for one atom ('C(1)') very large. Problems with refinement?
1 Two Uij values stand out. Manual data entry error? Uij multiplied by 1E4?
1 Two Uij values stand out. Manual data entry error? (Typed "9" instead of "0"?)
1 Two Uij values stand out. Manual data entry error?
1 Three Uij values stand out. Manual data entry error? Uij multiplied by 1E4?
1 The first (U11) value on *some*, but not *all*, hydrogens seems to be converted to B instead of U (???)
1 Some atoms seem to have Uij, some probably have Biso specified as U11. Manual data entry error?
1 Reason for large Uij not clear at all. Similar to 1544873
1 Reason for large Uij not clear at all.
1 Possible reason
1 One Uij value stands out. Problems with refinement?
1 One Uij value stands out. Manual data entry error? Or refinement problems?
1 One Uij value stands out. Manual data entry error? Digits missing from some Uij values?
1 One Uij value stands out. Manual data entry error?
1 Large negative U23 for some atoms. Problems with refinement?
1 Heavy atoms seem to have Uij, hydrogens probably have Biso specified as U11. Manual data entry error?
1 Extra digits for some Uij values? Manual data entry error?
1 Digits missing from some Uij values? Problems with refinement?
1 Digits missing from some Uij values? Manual data entry error?
1 Biso instead of Uiso; problems with orthogonalisation?
1 Biso instead of Uiso; bad orthogonalisation?
1 Biso instead of Uiso. Uij multiplied by 1E4?
-------------- next part --------------
A non-text attachment was scrubbed...
Name: grazulis.vcf
Type: text/x-vcard
Size: 4 bytes
Desc: not available
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20200113/81c21705/attachment.vcf>
More information about the Cod-bugs
mailing list