This week saw the launch by the partners (, , and ) of a new, integrated (D&A) that supports structures determined using 3DEM, NMR as well as X-ray, neutron and electron crystallography. In this “D&A Q&A� blog, Gerard Kleywegt discusses some of the questions that depositors of PDB, EMDB and BMRB data at PDBe (especially those located in Europe and Africa) may have about how this will impact them.
What are the main advantages of this new D&A system?
A major advantage is that the new system is integrated so that it handles joint deposition of atomic coordinates (PDB) and EM electron-density maps (EMDB) or NMR experimental data (BMRB). PDB, EMDB and BMRB accession codes will be issued by the system as appropriate immediately after a structure has been deposited. Another major improvement over the older systems is that validation has become a core component. It will generate and request review of validation reports that implement recommendations for , and structures. Other improvements relate to the way ligands are handled, how coordinates are replaced, and how communication between depositors and curators takes place. Many crystallographers have been depositing data over the past two years using the new system and have enjoyed these advantages already. With the release of the integrated system, the same benefits extend to depositors of EM and NMR data.
What is the initial feedback from depositors?
Of course a lot of internal testing was done at all stages of development by developers and annotators at all wwPDB sites. Moreover, the X-ray system has been in production for two years and feedback from depositors worldwide has helped make this a mature system. Over the past few months, the NMR and EM components of the new system have been trialled by volunteers from a number of labs, including the team of (Switzerland). According to Nenad: �We like the new system a lot. It is nicely streamlined with simultaneous and integrated deposition of data to PDB and EMDB, which makes deposition easier and quicker and will hopefully stimulate more people in the EM field to deposit their data.�
Can I still deposit at PDBe using the older systems (AutoDep, EmDep)?
The old systems will remain in place for some time, at least until the middle of 2016. When these old systems are finally mothballed, there will of course be a grace period for users to finish pending depositions.
Where will my structures be annotated?
With the new system, the wwPDB has moved to a model where the annotation site is determined by the location of the depositor. This ensures that communication and support do not suffer too much from large time-zone differences. PDBe will handle all structures deposited by labs in Europe and Africa. However, structures that are still deposited with the legacy systems (AutoDep, EmDep, Adit-NMR) will continue to be annotated at the deposition site.
Will validation reports for all NMR and EM structures become available?
When the X-ray-only version of D&A was launched, the reports for all X-ray structures in the PDB were made available a few months later. We are currently recalculating all distributions and validation statistics and will release up-to-date validation reports for all X-ray, NMR and EM structures in the PDB archive in a few months� time.
Will there be a stand-alone validation server for NMR and EM structures?
The stand-alone wwPDB validation server for X-ray structures has been operational for over two years. Once the new deposition and annotation system is stable, work will begin to replace the validation server so it can handle NMR and EM structures as well.
Now that mmCIF is the official wwPDB coordinate format, can I still upload structures in the old PDB format?
The D&A system has been designed to handle a variety of common formats for structures and data. Structures in the old PDB format can still be uploaded and this will remain possible for the foreseeable future, until the community, represented by the , tells us otherwise.
Where do I go to deposit data with the new system?
To access the new deposition system, go to . There is also a available.
