To better support the increasing complexity and size of data submitted to the PDB archive, the wwPDB Deposition & Biocuration system is based on the PDBx/mmCIF data dictionary and file format. The system accepts, processes and distributes PDBx/mmCIF data files.
Depositors are encouraged to use the PDBx/mmCIF format for coordinate files whenever possible.
PDBx/mmCIF is the official working format of the wwPDB for coordinate files. It is flexible, extensible, and can accommodate structures of any size.
PDBx/mmCIF files ready for deposition are generated by most structure refinement programs. In the event where it is not possible to use a refinement program to generate PDBx/mmCIF files, the pdb_extract program may be used.
Additional information about the PDBx/mmCIF format can be found in this FAQ.
PDBx/mmCIF format is especially useful:
Depositors are encouraged to use the latest version of the refinement software packages to output up-to-date and mmCIF compliant deposition files.
Recent versions of refinement packages Phenix, REFMAC, and Buster generate PDBx/mmCIF files ready for deposition:
Phenix: Instructions are available at the Phenix website, https://www.phenix-online.org/documentation/overviews/xray-structure-deposition.html
CCP4: instructions are available for CCP4i2 (http://www.ccp4.ac.uk/deposition_ccp4i2) or
CCP4 Cloud (http://www.ccp4.ac.uk/deposition_ccp4cloud)
REFMAC (when using outside of CCP4i2 or CCP4 Cloud): To output a PDBx/mmCIF file from REFMAC, add a card that reads "pdbout format mmcif". REFMAC can also read a file by specifying a PDBx/mmCIF file as an HKLIN argument.
Buster: Instructions are available at the Buster website (https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif)
For non-crystallography depositions, the pdb_extract program is available as an online interface and as a standalone command-line program to convert PDB format file to PDBx/mmcif format. It extracts and harvests data in PDBx/mmCIF format from structure determination programs. To prepare PDB format data files for use with pdb_extract and the wwPDB deposition tool, please follow the instructions at OneDep FAQ.