Frequently Asked Questions

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. 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.

3. 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.

4. 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.

5. 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.

6. How do I contact PDB-Dev for deposition related issues?

Users can contact us via email (pdb-dev@mail.wwpdb.org). Please visit our contact page for more information.