Dear all,
Depositors can now submit structures directly to the wwPDB OneDep system
from within the structure determination software packages via a newly
developed*Deposition API*, combined with theOneDep Library
<https://github.com/wwPDB/onedep_lib>. This new capability represents
the first milestone of a wwPDB collaborative project involving the RCSB
PDB, PDBe, and EMDB, and developers of the Phenix, CCP4, CCP-EM, and
Global Phasing software suites. It strives to streamline the deposition
workflow by allowing users to initiate depositions without leaving their
structure determination software environment. The functionality is
currently available in*Phenix*and*CCP-EM Doppio*, with support in
the*CCP4*and*Global Phasing*software packages coming soon.Documentation
describing how to use these tools for direct deposition is available
<https://wwpdb.github.io/onedep_lib/>.
The broader objective of this collaborative project is to develop a
comprehensive set of interoperable tools that simplify and automate the
deposition processes while improving data quality and consistency. The
next phase of the project will focus on enabling structure determination
software packages to provide additional metadata, including
macromolecule and small-molecule annotations, to complete deposition
requirements. This innovation will allow software suites to generate
complete, deposition compliant, and metadata-rich mmCIF files that can
be deposited directly to and processed by OneDep, significantly reducing
manual data entry through the OneDep user interface for X-ray
crystallographic and 3DEM atomic coordinate models and underlying
experimental data and metadata.
In the longer term, these capabilities will support the direct
deposition of multiple related structures generated during structural
biology investigations, together with enriched structure- and/or
project-specific information. This integrated workflow is also expected
to improve efficiency, reduce deposition time, and provide a more
seamless experience for depositors.
We encourage depositors to explore the new direct deposition
functionality and provide feedback [email protected] the
relevant support contacts of the different structure determination
packages. Community feedback will help guide future enhancements and
ensure these tools meet the evolving needs of the structural biology
community.
Kind regards,
Deborah Harrus, on behalf of the wwPDB
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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