[Cod-bugs] Possible COD errors

[Saulius Gražulis]

Hi, Bob,

I've looked through your sample. Below ar my thoughts
On 2018-04-12 13:26, Robert McMeeking - UKRI STFC wrote:
> 2000430
> Coordinate error
> H(18B) 3956(9) .328(2) .0914(12) .049(7)
> and possibly others

The typo is in the original file
(http://scripts.iucr.org/cgi-bin/sendcif?al0527sup1); we need to look a
the original paper or contact authors to fix that;

> 1517953
> Coordinate error
> H41 H -003915(69) 0.1170(37) 0.3539(45) 0.033(5)
> and possibly others

Deposited by our colleagues; we'll contact them to see of they have
correct files, or can update coordinates. But, since the file was fro ma
published paper, most probably the error is upstream.

> 2100824
> Coordinate error
> Cl(76) 1109(8) .7910(10) .718(2) .078(6)
> and possibly others

The typo is in the original
(http://scripts.iucr.org/cgi-bin/sendcif?as0591sup1), ; we need to look
a the original paper or contact authors to fix that;

> 2104629
> No Cell data
The cell data is missing from the original
https://doi.org/10.1107/S0108768109032728/hw5005sup1.cif; it is a hybrid
method structure for which probably the cell is not well defined anyway.
I must admit however that other data sets from the same paper ave very
buggy (some *.txt files do not even compile as CIFs), so I doubt the
possibility to make use of that data...

> 4020454
> loop_
> _symmetry_equiv_pos_as_xyz
>   +x,+y,+z  1/2-x,-y,1/2+z  1/2+x,1/2-y,-z  -x,1/2+y,1/2-z
> 
> 4100182
> loop_
> _symmetry_equiv_pos_as_xyz
>   +x,+y,+z  +x,-y,-z  -x,-y,+z  -x,+y,-z  +y,-x,-z  -y,-x,+z  -y,+x,-z  +y,+x,+z
> etc.

These two seem OK for me...

> 4342694
> loop_
> _space_group_symop_id
> _space_group_symop_operation_xyz
> x,y,z -x,-y,-z

Here, symop IDs are missing; seems like they were not inserted during
the data curation. Fixed in COD rev. 207319.

> 8103028
> loop_
> _symmetry_equiv_pos_as_xyz
> x,y,z  -x,y,z  x,-y,z  -x,-y,z

This is a totally messed up CIF, with ';' text field marks placed
incorrectly. We need to get to the authors to fix that, and even then
it's rather hopeless, I guess...

In summary – 1 file fixed, 2 files seem OK (need more specific bug
report), all other have upstream errors with varying degree of
possibilities to correct them.

Cheers,
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