File Formats and the PDB

Freezing the PDB Format

  • PDB entries have been distributed in PDBx/mmCIF file format since it became the standard PDB archive distribution format in 2014.
  • The PDB file format has not been modified or extended to support new content since 21 November 2012 - Format Content Guide Version 3.30 (Nov. 21, 2012).
  • The PDB file format is now frozen, and no future changes will be made.
  • As the PDBx/mmCIF format continues to evolve, PDB format files will become outdated.
  • The wwPDB will continue to accept data in PDB format for NMR and EM depositions only, provided that the input file format meets Format Content Guide Version 3.30. All deposited data will be captured, processed and distributed in PDBx/mmCIF format.
  • The wwPDB will continue to distribute data in PDB file format following Format Content Guide Version 3.30, where possible.
    • For entries that cannot be fully represented in the PDB file format, data will only be available in the PDB archive as PDBx/mmCIF-formatted files. This includes large entries that do not fit the PDB file format (those containing >62 chains and/or >99999 ATOM records). Where possible, these entries will also be distributed in "bundled" TAR files containing a collection of best effort/minimal files in PDB file format.

Master Format and PDBx/mmCIF Content Extension

  • PDBx/mmCIF (mmcif.wwpdb.org) is the official wwPDB working format and the standard PDB archive format.
  • All PDB data processing and annotation are performed using PDBx/mmCIF file format.
  • PDBx/mmCIF format imposes no limitations on the number of atoms, residues, or chains that can be included in a single PDB entry.
  • PDBx/mmCIF file format is being continually extended to include new content, while ensuring backwards compatibility.
  • Each data item in a PDBx/mmCIF file is precisely defined in the PDBx/mmCIF Exchange Data Dictionary.
  • The content of in the PDBx/mmCIF Exchange Data Dictionary is fully software accessible.
  • wwPDB continues to work with the PDBx/mmCIF Working Group to ensure that new data items are defined in the dictionary and captured in refinement output files in PDBx/mmCIF format.

Outreach in Community and Developer Engagement

  • Data Generation
    • The wwPDB continues to engage the refinement software PDBx/mmCIF Working Group to output deposition files in PDBx/mmCIF format. The major X-ray refinement software packages (Refmac and Phenix) can output data in PDBx/mmCIF-format files. Depositors are encouraged to output PDBx/mmCIF format files at the end of refinement process and use them directly for PDB deposition. SHELX, CNS, and BUSTER software developers are also encouraged to output PDBx/mmCIF files.
    • The NMR Exchange Format Working Group has established the NMR Exchange Format (NEF) as a unified, open standard format for the representation of NMR restraint and chemical shift data.
      • The wwPDB continues to accept and disseminate chemical shifts in NMR-STAR format and restraints in NMR-STAR and other formats.
      • A group of leading NMR spectroscopy software developers has committed to making their software capable of both reading and writing NEF-compliant files.
      • BMRB is working closely with the wwPDB NMR Validation Task Force (VTF) and the NEF Working Group to ensure interoperability with NMR-STAR for chemical shift and restraint deposition in the PDB archive.
      • The wwPDB will continue to work with NMR software developers to output PDBx/mmCIF format files for atomic coordinate files.
    • Similarly, the wwPDB will work with the 3D Electron Microscopy community to ensure development of software capable of reading and writing PDBx/mmCIF files.
  • Data Use
    • PDBx/mmCIF file format is supported by visualization applications such as Jmol, JSmol, Chimera, COOT, PyMol, CCP4MG, Molmil, and OpenRasMol.
    • For other software and bioinformatics resources services that use PDB data, such as CATH, UniProt/NCBI, etc., the wwPDB will continue to encourage these services to adopt PDBx/mmCIF files.
    • The wwPDB will continue to make PDBx/mmCIF software tools available to our User community, including format conversion tools.