[Cod-bugs] COD conversion with HighScore

Thomas Degen thomas.degen at panalytical.com
Mon Jan 13 09:27:25 EET 2020

Dear Saulius,

> Do you take Bij values after transforming them to an orthogonal frame, or in the original CIF Uij frame of reference?
We convert displacement parameters (and their standard deviations) from any source from U or Beta to B.
Where U to B is a factor 8*Sqr(Pi) an Beta to B is like that:

    Atom.B11.Value := 4 * (Beta11.Value / Sqr(ReciprocalAxis.a));
    Atom.B22.Value := 4 * (Beta22.Value / Sqr(ReciprocalAxis.b));
    Atom.B33.Value := 4 * (Beta33.Value / Sqr(ReciprocalAxis.c));
    Atom.B12.Value := 4 * (Beta12.Value / ReciprocalAxis.a * ReciprocalAxis.b);
    Atom.B13.Value := 4 * (Beta13.Value / ReciprocalAxis.a * ReciprocalAxis.c);
    Atom.B23.Value := 4 * (Beta23.Value / ReciprocalAxis.b * ReciprocalAxis.c);

And then keep them like that in our document.

Best regards,


-----Original Message-----
From: Saulius Gražulis <grazulis at ibt.lt>
Sent: Sunday, January 12, 2020 6:01 PM
To: Thomas Degen <thomas.degen at panalytical.com>; Thomas Dortmann <thomas.dortmann at panalytical.com>; cod-bugs at ibt.lt
Cc: Thomas Dortmann <thomas at tdsonline.nl>
Subject: Re: [Cod-bugs] COD conversion with HighScore

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,

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 email and any files transmitted with it are confidential and maybe legally privileged. Such message is intended solely for the use of the individual or entity to whom they are addressed. Please notify the originator of the message if you are not the intended recipient and destroy all copies of the message. Please note that any use, dissemination, or reproduction is strictly prohibited and may be unlawful.

This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

More information about the Cod-bugs mailing list