Remediation of 3DEM Entries in the Protein Data Bank
The wwPDB and the EMDataBank/Unified Data Resource for 3DEM Project (https://www.ncbi.nlm.nih.gov/pubmed/26578576) are collaborating to update the experimental methods descriptions of all electron microscopy and electron crystallography-derived structures in the PDB archive. When completed, all 3DEM-derived entries will have better organized content and will conform to the revised data model developed by the EMDataBank team for use within the wwPDB OneDep System. Since January 2016 the OneDep system (http://wwpdb.org/deposition/system-information) has supported deposition, annotation, and validation of 3DEM structures and fully integrates deposition of 3DEM maps and model coordinates.
Examples of remediated model files will be provided in a new wwPDB ftp directory (ftp://ftp.wwpdb.org/pub/pdb/test_data/EM/) and the corresponding PDBx/mmCIF dictionary will be released in December 2016. Files in the current PDB ftp archive will be replaced with new files corresponding to the updated PDBx/mmCIF dictionary in 2017. Users are encouraged to review and test the example data files.