2016 Remediation of 3DEM Entries

12/14 wwPDB News

The wwPDB and the EMDataBank/Unified Data Resource for 3DEM Project have collaborated to update the experimental methods descriptions of all electron microscopy and electron crystallography-derived structures in the PDB archive. With this work now completed, all 3DEM-derived entries have better-organized content and conform to the revised data model developed by the EMDataBank team for use within the wwPDB OneDep System. The OneDep System has supported deposition, annotation, and validation of 3DEM structures and fully integrates deposition of 3DEM maps and model coordinates since January 2016.

Examples of 3DEM model files (both remediated and from the OneDep system) are provided in a new wwPDB ftp directory ( A data-item level description of the changes made during remediation is provided here. 3DEM terms in the updated PDBx/mmCIF dictionary can be reviewed here.

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.

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