[Cod-bugs] COD conversion with HighScore

[Saulius Gražulis]

Dear Thomas,

I have just fixed a stupid bug in my cif_Uiso script (the script would
not get cell angles other than 90 degrees).

Now the agreement between Uiso(CIF) and Ueq is better :). Also, I now
see why my orthogonalisation did not work.

I will recalculate the tables.

On 2020-01-03 15:30, Thomas Dortmann wrote:
>  2. We check the values of Biso and Baniso, and we also convert
>     Baniso-values back to Biso values; 
> 
> in COD entry 9014636 there are very big Uaniso-values (converted into
> Baniso values > 10), but small Uiso-values?

I think my code now shows what you mean:

> saulius at varanas Uiso/ $ cod-download -s 9014636 | ./cif_Uiso 
> #DATABLCK :	9014636
> #SPCGRP   :	C 1 2/m 1
> #CELL     :	9.3720	17.6312	5.2732	90	102.247	90
> #@ label 	Uiso(CIF)	Ueq(comp)	Beq(comp)	diff
> NaA	     0.04154	    0.416959	     32.9218	   -0.375419
> NaAm	     0.03002	    0.299077	     23.6142	   -0.269057
> LiM4	     0.02014	     0.20043	     15.8253	    -0.18029
> NaM4	     0.02014	     0.20043	     15.8253	    -0.18029
> CaM4	     0.02014	     0.20043	     15.8253	    -0.18029
> MgM1	     0.00684	   0.0720588	     5.68954	  -0.0652188
> FeM1	     0.00684	   0.0720588	     5.68954	  -0.0652188
> ZnM1	     0.00684	   0.0720588	     5.68954	  -0.0652188
> AlM2	     0.00532	   0.0504816	     3.98587	  -0.0451616

I am not sure why this is so. Unfortunately, the original paper has no
accompanying CIF, and I can not get the original paper. I'll ask Bob
Downs what they did with this structure. Could be a typo.

> Questions: does the COD apply a sanity check on the supplied B (or U)
> values, and do you compare anisotropic with isotropic values?

So, the answer now is: we start do do this, with your help ;). However,
in case if discrepancies in the published structures, we can probably
only flag them, but not correct – unless the authors provide a
re-refined version.

Regards,
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

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