[3dem] New tools support deposition of structures to the wwPDB PDB and 3DEM Core Archives directly from structure determination software packages

[Justin Flatt]

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 the OneDep Library [1]. 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 [2].

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 to deposit-help at mail.wwpdb.org or 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.

Links:
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[1] https://urldefense.com/v3/__https://github.com/wwPDB/onedep_lib__;!!Mih3wA!ErwMTLMmZ1vKHU3hsQ6AB973UUx-MHEUvILONkroclUNPvEr4DWvcjEGSzpAajXZ8fgNF98xh1LEiyapBqs5j-Vj$ 
[2] https://urldefense.com/v3/__https://wwpdb.github.io/onedep_lib/__;!!Mih3wA!ErwMTLMmZ1vKHU3hsQ6AB973UUx-MHEUvILONkroclUNPvEr4DWvcjEGSzpAajXZ8fgNF98xh1LEiyapBsPBfq31$ 
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