Consistent Format for Validation and Coordinate Data

06/01 wwPDB News

wwPDB validation reports are now provided in PDBx/mmCIF format for all new depositions in OneDep. This change makes validation data more interoperable with the PDB archival format. Data are more logically and better organized in the PDBx/mmCIF reports, and therefore more “database-friendly” than the report in XML format. PDBx/mmCIF-format validation reports for newly released and modified entries will be distributed through the PDB and EMDB Core Archives.

The new PDBx/mmCIF reports are easier to interpret. They contain a high-level summary and offer easier access to residue-level information. Data are provided at multiple levels: entity, chain-specific, and even at the individual residues. For example, it is more straightforward to obtain the total number of clashes. The corresponding validation dictionary is available at Examples of PDBx/mmCIF validation reports for X-ray, 3DEM, and NMR are publicly available at GitHub.

PDBx/mmCIF validation reports will be provided for the full PDB and EMDB archives once archival validation recalculation is performed.

wwPDB strongly recommends all PDB users and software developers adopt this format for future applications.

News Index