wwPDB Welcome to the Worldwide Protein Data Bank
Access the PDB FTP:
RCSB PDB | PDBe | PDBj
Archive Download
Chemical Component Dictionary
Biologically Interesting Molecule Reference Dictionary (BIRD)
New Deposition and Annotation System
Tutorial
System Information
FAQ
Validation Reports
Reports
Server Information
Deposit Data to the PDB:
RCSB PDB | PDBe
PDBj | BMRB
Search for Structures:
RCSB PDB | PDBe
PDBj | BMRB
PDB Archive Snapshots:
RCSB PDB | PDBj
Instructions to Journals
Documentation: Format, Annotation and Policies, Remediation
Workshops and Task Forces
X-ray Validation
NMR Validation
EM Validation
SAS Task Force
PDBx/mmCIF Working Group
Past Symposia
Int'l Year of Crystallography
wwPDBAC
EMDB

PDBx/mmCIF Working Group

A working group has been established to enable the direct use of PDBx/mmCIF format files in the major macromolecular crystallographic software tools and to provide recommendations on format extensions required for deposition of large structures to the PDB.

The Working Group has made recommendations about essential extensions required for large structures (announced May 2013). PDBx/mmCIF files suitable for deposition can now be created with recent versions of the CCP4 (REFMAC 5.8) and Phenix (1.8.2) software packages. Both packages support these recommended extensions for large structures.

Members of the PDBx/mmCIF Working Group are:

  • Paul Adams, LBL (Phenix), Chair
  • Pavel Afonine, LBL (Phenix)
  • Helen Berman, RCSB PDB
  • Paul Emsley, Oxford University (Coot)
  • Rasmus Fogh, Cambridge University (CCPN)
  • Richard Gildea, LBL (Phenix)
  • Gerard Kleywegt, PDBe
  • Eugene Krissinel, STFC (CCP4)
  • Garib Murshudov, LMB-MRC (REFMAC)
  • Tom Oldfield, PDBe
  • Oliver Smart, Global Phasing (BUSTER)
  • Sameer Velankar, PDBe
  • John Westbrook, RCSB PDB

2011 Meeting

At a September 2011 meeting held at PDBe, the wwPDB met with key software developers to discuss the limitations of the PDB file format in its ability to support data for large structures, complex chemistry, and new and hybrid experimental methods.

Rather than designing an entirely new format, the consensus among developers was to actively switch to the PDBx/mmCIF format, particularly for use in deposition. A meeting outcome was the formation of this working group for the adoption of the PDBx/mmCIF format for deposition and as an exchange format between programs for macromolecular crystallography. Making it easier to capture more information in deposition and archiving will be part of this process.

Hinxton format meeting

2011 Workshop Participants

Top row: Sameer Velankar, Paul Adams, Randy Read, Thomas Womack, John Westbrook, Gerard Kleywegt, Eugene Krissinel
Middle row: John Ionides, Garib Murshudov, Helen Berman, Gerard Bricogne, Tom Oldfield
Bottom row: Oliver Smart, Paul Emsley, Ralf Grosse-Kunstleve


© wwPDB