[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