Mandatory PDBx/mmCIF format files submission for MX depositions

02/19 wwPDB News

Submission of PDBx/mmCIF format files for crystallographic depositions to the PDB will be mandatory from July 1st 2019 onward. PDB format files will no longer be accepted for deposition of structures solved by MX techniques.

PDBx/mmCIF will be the only format accepted for deposition of PDB structures resulting from macromolecular crystallography (MX), including X-ray, neutron, fiber, and electron diffraction methods via OneDep starting July 1st 2019. The deposition of PDBx/mmCIF format files will improve the efficiency of the deposition process and enhance validation through capture of the more extensive experimental metadata supported by PDBx/mmCIF, compared to the legacy PDB format. PDB entries with 100,000 or more atoms, and those with multiple character chain IDs are already not supported by the legacy PDB format. In addition, by 2021, we anticipate the PDB Chemical Component Identifier will need to be extended beyond three characters, which will necessarily result in full retirement of files in the PDB Core Archive that utilize the legacy PDB format.

Refmac, Phenix.refine, and Buster programs can now output PDBx/mmCIF formatted files. For users of other structure determination/refinement software packages, the wwPDB provides stand-alone and web-based tools to convert legacy PDB format files into PDBx/mmCIF format: pdb_extract and MAXIT. More information on outputting and preparing PDBx/mmCIF format files for deposition can be found on the wwPDB website.

The PDBx/mmCIF Working Group has committed to the PDBx/mmCIF data model. PDBx/mmCIF is also supported by visualization software applications, including Jmol/JSMol, LiteMol, Chimera, OpenRasMol, CCP4MG, COOT, PyMOL, VMD, MolMil, and NGL. In addition, other data resources, such as the Protein Model Portal and SASBDB, have adopted and extended the PDBx/mmCIF framework for data representation.

If you have any queries or comments regarding these changes, please contact the wwPDB consortium via

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