[Cod-bugs] Errors with files 6000694 and 6000695

Saulius Gražulis grazulis at ibt.lt
Tue Dec 5 09:13:21 EET 2017

Dear Luis,

thank you for your message!

On 2017-12-05 04:27, Luis Ortega San Martin wrote:
> I am a regular user of COD database and I have just found two cif files
> with errors: 6000694 <http://www.crystallography.net/cod/6000694.html>
> and 6000695 do not contain any atoms inside.
> I hope you can correct this.

The absence of coordinates is actually not a bug but a feature. COD
stores as much information as we can get from published sources, and for
some entries coordinates were not available at the point of deposition.
There are more entries like this in COD; you can select them (or filter
them out) using the SQL database table `data` column 'flags', e.g.:

> saulius at koala ~/ $ mysql -u cod_reader -h sql.crystallography.net cod -e 'select count(*) from data where flags not like "%has coordinates%"'
> +----------+
> | count(*) |
> +----------+
> |     1375 |
> +----------+

or by analysing _atom_site_fract_x, ..._y and ..._z data items (they
contain special CIF values '?').

In due time, we hope to get all original publications for these
structures and deposit the coordinates, but this is done on the best
effort basis. You can help to improve COD if you have access to (some)
of these publications and can send us the atomic coordinates, preferably
in CIF format.

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

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