[Cod-bugs] COD conversion with HighScore

[Saulius Gražulis]

Dear Thomas,

thank you for the clarifications!

On 2020-01-11 18:47, Thomas Degen wrote:
> No, it is what it says, it is about how often any of the anisotropic values (B11,B22,B33,B12,B23,B13) hit the "B >= 10" limit.

I see. I misread the table, assuming 'Banis' is in fact Beq computed
from Bij.

Now I can mostly get the same counts as in your table; occasionally I
still get somewhat less Bij >= 10 as in your table (e.g. for COD 7123444
I get 51 large Bij value instead of 54). But the results are now very
similar, so I can proceed with the survey of the issues.

Do you take Bij values after transforming them to an orthogonal frame,
or in the original CIF Uij frame of reference?

> We are using B instead of U in the UI because these values are closer to 1, which makes them more convenient to look at.

OK, clear. * 8 * pi ** 2 ?

>> Could you please send my your code example
> This is approximately the code to convert Banis to Biso:
> 
> case FSpaceGroup.SimpleCrystalSystem of
>         scTriclinic:
>           begin
>             Atom.Biso.Value := (1 / 3) *
>               (Atom.b11.Value * Sqr(Cell.a * ReciprocalCell.a) + Atom.b22.Value * Sqr(Cell.b * ReciprocalCell.b)
>               + Atom.b33.Value * Sqr(Cell.c * ReciprocalCell.c)
>               + 2 * Atom.b12.Value * Cell.a * Cell.b * ReciprocalCell.a * ReciprocalCell.b * CosDeg(Cell.gamma)
>               + 2 * Atom.b13.Value * Cell.a * Cell.c * ReciprocalCell.a * ReciprocalCell.c * CosDeg(Cell.beta)
>               + 2 * Atom.b23.Value * Cell.b * Cell.c * ReciprocalCell.b * ReciprocalCell.c * CosDeg(Cell.alpha));
>           end;

Perfect. This is the same formula as Fischer1988 describes, and which I
use as well. The values should be reproducible (even though I do not use
special cases for higher-symmetry groups).

> 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).

In some cases, the unites are indeed mixed up, but I now find a bunch of
other reasons. I'll let you know in a follow-up mail.

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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 213 bytes
Desc: OpenPGP digital signature
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20200112/fb6c0cb0/attachment.sig>