PDB Focus: the ADIT Validation Server

Depositors are encouraged to use the ADIT Validation Server (http://pdb.rutgers.edu/validate/) prior to the deposition of a structure to the PDB. The Validation Server may be used to check a structure at any time during structure determination and refinement. There is no limit to the number of times it can be used.

The RCSB developed the Validation Server to allow users to check the format consistency of coordinates (Precheck) and to create validation reports about a structure before deposition (Validation).

To use the Validation Server, the coordinate file should be in either PDB or mmCIF format. The structure factor file must be in mmCIF format (see http://pdb.rutgers.edu/sf_cif.html for more information).

The Precheck step will produce a brief report identifying any changes that need to be made in your data files in order to obtain a validation report.

The Validation step produces a validation report which includes an Atlas entry, a summary report, and a collection of structural diagnostics including bond distance and angle comparisons, torsion angle comparisons, base morphology comparisons (for nucleic acids), and molecular graphic images. Reports from PROCHECK (Laskowski et al. 1993), NUCheck (Feng et al. 1998), and SFCheck (Vaguine et al. 1999) are made available.

Tutorials are available online at http://pdb.rutgers.edu/validate/docs/tutorial.html.

Laskowski, RA, McArthur, MW, Moss, DS, and Thornton, JM. J. Appl. Cryst., 1993; 265:283-291.
Feng, Z, Westbrook, J, and Berman, HM. NUCheck. 1998. NDB-407 Rutgers University, New Brunswick, NJ.
Vaguine, AA, Richelle, J, and Wodak, SJ. Acta Crystallogr., 1999; D55:191-205.