Crystallographic Structure Deposition


Once a crystallographic structure is solved it is usually deposited in the World Wide Protein Data Bank (wwPDB). This is necessary for publication as most journals require a PDBID to be included in any manuscript under review that describes a new crystallographic structure. The wwPDB is an invaluable resource that contains over 150,000 structures (as of June 2019).


The model files (PDB and mmCIF) generated by phenix.refine contain information that is required when depositing a structure to the wwPDB. Starting in July 2019, the wwPDB will only accept model files in mmCIF for deposition.

To generate a model file suitable to deposition, a two stage process is currently recommended:

  1. By default, phenix.refine will output model files in mmCIF and PDB format. If you turned off the option for mmCIF output, run a final cycle of phenix.refine that writes mmCIF files for model and data (this can be set in the Output section of the GUI).
  2. The model file (mmCIF) and a sequence file can then be processed with mmtbx.prepare_pdb_deposition program to create a mmCIF file with the sequence. This program requires the full sequence for the macromolecule to be provided. In the GUI, this program is in the "PDB Deposition" section of tools.

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