Archival PDBx/mmCIF Version V4 to V5 Update in the Protein Data Bank
The wwPDB is preparing the update of PDBx/mmCIF model files for all entries in the PDB archive to V5 version of the PDBx/mmCIF dictionary. When completed, all PDB model files will have better organized content and will conform to the revised data model used within the wwPDB OneDep System. A list of changes will be available at the wwPDB website (https://www.wwpdb.org/documentation/remediation). Since January 2016, the OneDep system (https://www.wwpdb.org/deposition/system-information) has supported Deposition, Biocuration, and Validation of structures determined by experimental methods currently accepted by the PDB.
The updated model files for all experimental methods will be made available in a new PDB FTP server (ftp://ftp-beta.wwpdb.org/pub/pdb/data/structures/), and the corresponding PDBx/mmCIF dictionary will be released in May 2017. The test FTP area (ftp://ftp.wwpdb.org/pub/pdb/test_data/EM/) containing previously updated 3DEM model files (previously made available in December 2016) will be simultaneously retired.
The current PDB FTP archive will be updated with new files corresponding to the V5 PDBx/mmCIF dictionary in July 2017. Users are strongly encouraged to review and test the updated data files.