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.
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.
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.
Users need to be registered to deposit a new structure. New users can create an account by registering here. Existing users can login here. After logging in, users can start a new deposition, view ongoing depositions or view previously completed depositions from their account home page.
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.