[Cod-bugs] Cif files with incorrect set of group operators

[Saulius Gražulis]

Hi, Steef,

On 2023-02-22 10:07, Steef Boerrigter wrote:
> I have added a diff file of (today's) database entry with the fixed
> version of the cif. The diff file includes my analysis of what went
> wrong with the operators.
> I am also including the fixed cif files.

There is one more gotcha with the change of symmetry operators. The 
operator indices are used in _geom_bond and _geom_angle_ tables. When we 
change the symmetry operators, these _geom_ references are no longer 
valid. This is one of the reasons why we try not to modify symops in 
general.

But in the case of the 15 files that you have corrected, the initial 
symmetry operators where wrong, for one reason or another. Therefore we 
can not rely on the references to these operators in the _geom_ tables 
since we do not know what the authors meant. For this reason I will 
replace the '_geom_bond_site_symmetry_...' values and other similar 
values with question marks ('?', without the quotes), to indicate that 
these references are not know.

You do not need to do anything about this change (other than to make 
sure that your software tolerates CIFs with '?' values ;) ); I just 
inform you that I will make additional changes to the files you have sent.

Sincerely yours,
Saulius

-- 
Dr. Saulius Gražulis
Vilnius University, Life Science Center, Institute of Biotechnology
Saulėtekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania)
phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366


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