PDBCOP: PDB Comparison Program


Karla Fejfarová1*, Jan Dohnálek1,2, Jindřich Hašek2

1Institute of Macromolecular Chemistry AS CR, v.v.i., Heyrovského nám. 2/1888, 162 06 Prague 6, Czech Republic

2Institute of Biotechnology AS CR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic

* correspondence e-mail: fejfarova@imc.cas.cz


Crystallographic structure determination has become a technique that can be readily applied to many research problems in biotechnology, biomedicine, and drug design. These applications should be based on only the reliable data, however, some of the models in the Protein Data Bank still contain errors of various kinds [1]. It should be emphasized that one cannot blindly accept the results of automated crystal structure solution and refinement procedures and that it is essential to carefully assess the model quality.

The most common validation tools, MolProbity [2], and the wwPDB validation server [3], check mainly the geometric quality of the model. In the final stages of the crystal structure refinement, it is also important to keep track of those atoms, for which parameters change significantly during the refinement cycles. These atoms, usually belonging to solvent molecules, may be the source of possible problems. With the size of a typical macromolecular structure, it is almost impossible to check all the atoms manually.

PDBCOP is a command line-based tool that assembles specific details about X-ray structure model from PDB file. If called in mode with two input files, it compares two PDB files and prints a list of atoms, for which position or ADP changed more than a certain threshold. In mode with one input file, PDBCOP can list e.g. non-standard residues in the PDB file, all atoms with occupancy different from 0 and 1, and residues with alternate conformations. The Linux version of PDBCOP is available at http://crysa.fzu.cz/pdbcop/.

This work was supported by the Ministry of Education, Youth and Sports of the Czech Republic (grant No. EE2.3.30.0029), and by BIOCEV CZ.1.05/1.1.00/02.0109 from the European Regional Development Fund.


1.         Dauter Z., Wlodawer A., Minor W. et al., IUCrJ, 2014, 1, 179-193.

2.         Chen V. B., Arendall W. B., Headd J. J. et al., Acta Cryst., 2010, D66, 12-21.

3.         Berman H. M., Henrick K., Nakamura H., Nat. Struct. Biol., 2003, 10, 980.