1. What kind of models can be deposited to PDB-Dev?
We currently accept I/H models that follow the specifications defined in the I/H methods dictionary. The dictionary is a modular extension of the PDBx/mmCIF dictionary used in the PDB archive. This dictionary supports multi-scale, multi-state, time-ordered ensembles of macromolecular assemblies along with definitions for spatial restraints derived from a variety of experimental techniques. More information about the dictionary can be found here.
2. I have an experimental model determined using X-ray crystallography / NMR spectroscopy / Electron microscopy. Can I deposit my structure in PDB-Dev?
No. Experimental structures determined using X-ray crystallography or NMR spectroscopy or Electron microscopy should be deposited through the wwpdb OneDep system.
3. I have a computational model obtained using homology modeling or ab initio methods. Can I deposit my structure in PDB-Dev?
No. Purely computational models obtained using homology modeling or ab initio methods should be deposited in the Model Archive.
4. Where do I deposit the experimental data based on which my structure was determined?
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.
5. Are there any specific requirements for uploading files?
The model file has to be in a format compliant with the I/H methods extension of the PDBx/mmCIF dictionary. We do not accept I/H models in PDB format.
6. Are there any software programs that support the IHM-dictionary?
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.
7. Can these models be viewed using existing molecular visualization tools?
The structures in PDB-Dev can be downloaded and visualized using the UCSF ChimeraX visualization software, which provides built-in support for the new I/H methods data representation. Please use the daily build for the most up-to-date visualization and modify the file extension of the I/H structure file from "cif" to "ihm". Work is in progress to update other existing software to enable visualization of the I/H models. We recommend depositors to upload an image of their modeled structure along with the deposition.
8. How do I deposit a new structure?
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 click on the Deposit link to deposit a new structure or view exisiting depositions.
9. How do I delete a deposited structure?
Users need to login to their account for deleting a deposition. 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 deposition can be deleted. Alternately, users can contact us via email to manage their depositions.