PDBx/mmCIF Working Group
This Working Group provides guidance on dictionary content and promotes the standard among structural biology methods developers. The Working Group meets regularly with the wwPDB.
- Paul Adams, LBL (Phenix), Chair
- Paul Emsley, Oxford University (Coot)
- Nigel Moriarty, LBL (Phenix)
- Garib Murshudov, LMB-MRC (REFMAC)
- Gerard Bricogne, Global Phasing (BUSTER)
- Jeff Bell, Schrodinger
- Eugene Krissinel, STFC (CCP4)
- Nicholas Sauter, LBL (Phenix)
- Mike Word, OpenEye
- Rasmus Fogh, University of Cambridge (CCP4)
- John Ionides, WeNMR
The Working Group was initially established in 2011 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 (announced May 2013).
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.
Additional meetings and workshops have been hosted at PDBe and Rutgers.
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
PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology
John D. Westbrook, Jasmine Y. Young, Chenghua Shao, Zukang Feng, Vladimir Guranovic, Catherine L. Lawson, Brinda Vallat, Paul D. Adams, John M. Berrisford, Gerard Bricogne, Kay Diederichs, Robbie P. Joosten, Peter Keller, Nigel W. Moriarty, Oleg V. Sobolev, Sameer Velankar, Clemens Vonrhein, David G. Waterman, Genji Kurisu, Helen M. Berman, Stephen K. Burley, Ezra Peisach
(2022) Journal of Molecular Biology 434: 167599 doi: 10.1016/j.jmb.2022.167599
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)
Paul D. Adams, Pavel V. Afonine, Kumaran Baskaran, Helen M. Berman, John Berrisford, Gerard Bricogne, David G. Brown, Stephen K. Burley, Minyu Chen, Zukang Feng, Claus Flensburg, Aleksandras Gutmanas, Jeffrey C. Hoch, Yasuyo Ikegawa, Yumiko Kengaku, Eugene Krissinel, Genji Kurisu, Yuhe Liang, Dorothee Liebschner, Lora Mak, John L. Markley, Nigel W. Moriarty, Garib N. Murshudov, Martin Noble, Ezra Peisach, Irina Persikova, Billy K. Poon, Oleg V. Sobolev, Eldon L. Ulrich, Sameer Velankar, Clemens Vonrhein, John Westbrook, Marcin Wojdyr, Masashi Yokochij, Jasmine Y. Young
(2019) Acta Cryst. D75, 451-454. doi: 10.1107/S2059798319004522