Dear all,
Extensions to the PDBx/mmCIF dictionary for reflection data with
anisotropic diffraction limits, for unmerged reflection data, and for
quality metrics of anomalous diffraction data are now supported in OneDep.
In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group
<https://www.wwpdb.org/task/mmcif> was convened to develop a richer
description of experimental data and associated data quality metrics.
Members of this Data Collection and Processing Subgroup are all actively
engaged in development and support of diffraction data processing
software. The Subgroup met virtually for several months discussing,
reviewing, and finalizing a new set dictionary content extension that
were incorporated into the PDBx/mmCIF dictionary
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/> on
February 16, 2021. A reference implementation of the new content
extensions has been developed by Global Phasing Ltd.
<https://www.globalphasing.com/>
These extensions facilitate the deposition and archiving of a broader
range of diffraction data, as well as new quality metrics pertaining to
these data. These extensions cover three main areas:
1. scaled and merged reflection data that have been processed to take
account of diffraction anisotropy, by providing descriptors for that
anisotropy, in terms of (1) a parameter-free definition of a cut-off
surface by means of a per-reflection “signal” and a threshold value
for that signal, and (2) the ellipsoid providing the best fit to the
resulting cut-off surface;
2. scaled and unmerged reflection data, by providing extra item
definitions aimed at ensuring that such data can be meaningfully
re-analysed, and their quality assessed independently from the
associated model, after retrieval from the archive;
3. anomalous diffraction data, by adding descriptors for numerous
relevant, but previously missing, statistics.
The new mmCIF data extensions describing anisotropic diffraction now
enable archiving of the results of Global Phasing’s STARANISO program.
Developers of other software can make use of them or extend the present
definitions to suit their applications. Example files created by
autoPROC, BUSTER (version 20210224
<https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif>)
and Gemmi that are compliant with the new dictionary extensions are
provided in a GitHub repository
<https://github.com/pdbxmmcifwg/onedep-extended-sf-support-examples.git>.
These example files, and similarly compliant files produced by other
data processing and/or refinement programs, are suitable for direct
uploading to the wwPDB OneDep system. Automatic recognition of that
compliance, implemented by means of explicit dictionary versioning using
the new pdbx_audit_conform record, will avoid unnecessary pre-processing
at the time of deposition. This improved OneDep support will ensure a
lossless round trip between data processing/refinement in the lab and
deposition at the PDB.
wwPDB strongly encourages structural biologists to always use the latest
versions of structure determination software packages to produce data
files for PDB deposition. wwPDB also encourages crystallographers
wishing to deposit new structures together with their associated
diffraction data to use the software which guarantees consistency
between data and final model. This consistency is difficult to achieve
when separate diffraction data files and model coordinate files are
pieced together /a posterior/i by /ad hoc/ means.
wwPDB also encourages depositors to make their raw diffraction images
available from one of the public repositories
<https://www.wwpdb.org/deposition/faq#start> to allow direct access to
the original diffraction image data.
--
Regards,
Jasmine
===========================================================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
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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