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 many tens of thousands of structures, which are increasingly used to solve new crystal structures by molecular replacement.


The PDB files generated by phenix.refine contain information that is useful when depositing a structure to the wwPDB. However, a much better route is to deposit mmCIF format files, for both model and data. To do this, a two stage process is currently recommended: running 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). The model file and a sequence file can then be processed with mmtbx.prepare_pdb_deposition program (from the command line) to create a mmCIF file with the sequence. This program requires the full sequence for the macromolecule to be provided. The result of this will be a mmCIF file containing the model, and a mmCIF file containing the data. These files can then be directly uploaded as part of the wwPDB deposition process.

Common issues

Related programs