The wwPDB and the EMDataBank/Unified Data Resource for 3DEM Project
<https://www.ncbi.nlm.nih.gov/pubmed/26578576> have collaborated to
update the experimental methods descriptions of all electron microscopy
and electron crystallography-derived structures in the PDB archive. With
this work now completed, all 3DEM-derived entries have better-organized
content and conform to the revised data model developed by the
EMDataBank team for use within the wwPDB OneDep System
<http://wwpdb.org/deposition/system-information>. The OneDep System has
supported deposition, annotation, and validation of 3DEM structures and
fully integrates deposition of 3DEM maps and model coordinates since
January 2016.
Examples of 3DEM model files (both remediated and from the OneDep
system) are provided in a new wwPDB ftp directory
(ftp://ftp.wwpdb.org/pub/pdb/test_data/EM/). A data-item level
description of the changes made during remediation is provided here
<http://cdn.wwpdb.org/wwpdb/docs/documentation/remediation/summary-changes.xlsx>.
3DEM terms in the updated PDBx/mmCIF dictionary can be reviewed here
<http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v5_rc.dic/Groups/em_group.html>.
Files in the current PDB ftp archive will be replaced with new files
corresponding to the updated PDBx/mmCIF dictionary in 2017. Users are
encouraged to review and test the example data files.
We welcome your feedback. Please send any comments or questions to
deposit-h...@mail.wwpdb.org.
--
Regards,
Jasmine
===========================================================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
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