Crystallography Open Database

Crystallography Open Database

The COD structure - short introduction

The COD is built in a MySQL/PHP/Apache system from CIFs uploaded by crystallographers. These CIFS are first processed by the CIF2COD software which writes a .txt file containing the various fields used for the database search. The MySQL database (named 'cod') has only one table (named 'data') which is easily updated by uploading the above .txt file. There are 14 fields in the table defined as :

The 'entry' field starts at 1, and each time a new line is entered in the 'data' table, 'entry' is incremented by 1.

The 'file' field is a number between 1000000 and 9999999 which is used for the CIF file retrieving. Note that one CIF may contain several crystal structure (= several entries). Thus, the CIFs are named between 1000000.cif and 9999999.cif.

The 'pdf' file is either 1 or 0 if a PDF file exists or not, corresponding to a CIF file.

The fields 'a', 'b', 'c', 'alpha', 'beta', 'gamma', 'vol' (= volume), 'sg' (= space group) and 'formula' are explicit.

The field 'nel' contains the number of different elements in the chemical formula. Thanks to this field, searches can be made on strict numbers of elements (allowing more easily to retrieve binary or ternary compounds).

The field 'text' contains mineral names (if any), authors, reference and comments. If nothing is found in the CIF, that field contains the word 'unknown'.

COD is essentially a database for finding if your compound structure is already known, so that the search can be performed on the chemical composition and for volume and cell parameter ranges. 

Below is shown the COD database upload by adding fields in the .txt file :

Below is the content of the 2 first lines of the first created .txt file. Each field is enclosed by quotes "etc", and the fields are separated by the ; character. The line does not contain the 'entry' field, it starts at the 'file' field.

first line :
"1000000";"0";"   7.8783";"  10.4689";"  16.0680";" 90.000";" 95.147";" 90.000"
;"     1319.90";"  6 ";"P21/n";"C 5.00 H 17.00 O 8.00 N 2.00 P 2.00 Al 1.00"
a One-Dimensional Aluminophosphate"
second line :
"1000001";"0";"  48.4800";"  21.7200";"  10.7400";" 90.000";" 90.000";" 90.000"
;"    11309.10";"  4 ";"P 21 21 21";"C 107.00 H 142.00 O 26.00 N 14.00"
;"Alain Soyer  Pristinamycin complex solved using Shake-and-Bake"

Querying the COD is made by HTML forms and PHP scripts which directly connect to the MySQL part.

Example of part of PHP simple syntax code for requesting all entries between volumes vmin and vmax :

    $requete = "SELECT * FROM data WHERE vol BETWEEN $vmin and $vmax LIMIT 300";
It means that in the table "data", the field "vol" is searched for values comprised between vmin and vmax, stopping the search if more than 300 entries are found.

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Crystallography Open Database
Updated 17/03/2003