[Cod-bugs] Errors with files 6000694 and 6000695

Luis Ortega San Martin lortegas at pucp.edu.pe
Tue Dec 5 15:13:44 EET 2017

Dear Saulius,

Thanks for the rapid response and recommendations.

If I can get the structure of these two compounds I will send you the 
full CIF.

Thanks again


El 05/12/2017 a las 2:13, Saulius Gražulis escribió:
> 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,
> Saulius

Dr. Luis Ortega San Martin
Dpto. Ciencias, Sección Quimica
Pontificia Universidad Católica del Peru
Av. Universitaria, 1801. San Miguel
Lima 32. Peru
Tlf: +511 626 2000 ext.4227
alternative e-mail: luis.ortegasm at gmail.com

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