Frequently Asked Questions
We currently accept integrative or hybrid models that follow the specifications defined in the IHM dictionary. The dictionary is a modular extension of the PDBx/mmCIF dictionary used in the PDB archive. This dictionary supports multi-scale, multi-state, and ordered ensembles of macromolecular assemblies along with definitions for spatial restraints derived from a variety of experimental techniques.
No. Experimental structures determined using X-ray crystallography or NMR spectroscopy or Electron microscopy should be deposited through the wwPDB OneDep system.
No. Purely computational models obtained using homology modeling or ab initio methods should be deposited in the Model Archive.
The integrative / hybrid models and the associated spatial restraints should be deposited here at PDB-Dev and should comply with the definitions in the IHM dictionary.
The primary experimental data from which the spatial restraints are derived should be deposited in the corresponding experimental data repository. The following guidelines may be followed for depositing primary experimental data.
- NMR data (not accepted by the wwPDB OneDep system) can be deposited at BMRB.
- 3DEM map data can be deposited at EMDB.
- EM micrographs and 2DEM class averages can be deposited at EMPIAR.
- SAS data can be deposited at SASBDB.
- Proteomics data can be deposited at the ProteomeXchange Consortium.
The accession codes pertaining to these depositions should be included with the structure deposited in PDB-Dev.
In case there is no primary data repository corresponding to the experimental data used in the modeling, then the data should be referenced using a Digital Object Identifier (DOI). DOIs may be obtained from any provider. Zenodo is a DOI provider frequently used by PDB-Dev depositors.
The model file has to be in a format compliant with the IHM dictionary. We do not accept depositions in PDB format.
We provide a standalone software library called python-ihm that supports the new IHM dictionary. The library can be used to read and write data files compliant with the dictionary. Please see the documentation or some worked examples for more details.
Integrative modeling software such as IMP support the IHM dictionary. Work is in progress for other integrative modeling software such as HADDOCK to support the dictionary.
The structures in PDB-Dev can be downloaded and visualized using the UCSF ChimeraX visualization software, which provides built-in support for the new IHM data dictionary. Please use the daily build for the most up-to-date visualization and use the command line option "format ihm" to visualize multi-scale structures. For more details, please refer to the news item related to ChimeraX.
Integrative structures can also be visualized using the Molstar viewer. Molstar is an open collaboration started by PDBe and RCSB PDB to provide a technology stack for data delivery and analysis tools of macromolecules. Molstar viewer is now embedded within the PDB-Dev website and structures in PDB-Dev can be visualized through Molstar from the individual entry pages. Molstar can visualize atomic as well as multi-scale structures. For more details, please refer to the news item related to Molstar.
Work is in progress to support the visualization of integrative structures using other molecular visualization tools. We recommend depositors to upload an image of their modeled structure along with the deposition.
Structures that have been released cannot be deleted. For deleting other depositions, users need to login to their account. After logging in, click on the "view completed depositions" link provided in the user account page. Then, choose the deposition to be deleted. On the corresponding deposition page, a link is provided to delete the deposition. At the moment, individual files cannot be deleted. Only the entire depositions can be deleted. Alternately, users can contact or email us to manage their depositions.
To cite PDB-Dev, please use one of the following references:
Vallat B et al., Acta Cryst. 2021; D77: 1486-1496, doi: 10.1107/S2059798321010871
Vallat B et al., Structure. 2018 Jun; 26(6):894-904, doi: 10.1016/j.str.2018.03.011.
To cite a structure from PDB-Dev, please use the primary citation of the structure and the PDB-Dev accession code.
Yes. Once the deposition is processed, an accession code is issued, after which the entry can either be released or kept on hold. Following wwPDB policies, entries can be placed on hold for a maximum period of one year from the date of deposition. If an entry remains unreleased at the end of the hold period, it must either be released or withdrawn.
We have developed a new Data Harvesting System that provides a web interface for depositors to assemble all the information required for archiving integrative structures in PDB-Dev and to create a compliant mmCIF file. This includes the submission of integrative structures, associated spatial restraints and starting models used, modeling protocols and metadata information (citations, authors, software, data in external repositories, reference sequence information etc.).
The data harvesting system provides an automated mechanism for collecting diverse and heterogeneous types of integrative structures and restraint data. The system has been developed using the DERIVA scientific asset management platform and is based on the definitions in the IHM-dictionary and the parent PDBx/mmCIF dictionary.
A User Guide has been created with documentation regarding creating accounts and submitting data.
Users are encouraged to provide any feedback via email to pdb-dev@mail.wwpdb.org.