Reviewers are requesting that we deposit HADDOCK models in the PDB-Dev archive prior to publication. Does the HADDOCK pipeline currently use python-ihm to automatically generate mmCIF files for PDB-Dev deposition?
Many thanks for your input,
I heard PDB-Dev has a new beta deposition interface that should make your life easier
The server does allow to download mmCIF files. But only per model.
They will only contain limited information.
I suggest you contact Brinda Vallat (email@example.com). You might get to test then the new interface.
I’d just emailed Brinda about the new deposition interface - that would sure make things easier .
I also emailed Ben Webb about how to use the python-ihm modules and he seemed to think that they had been already added to the HADDOCK pipeline to automatically generate mmCIFs suitable for deposition in PDB-Dev. From what you say about the downloadable mmCIFs only containing limited information, I presume that they wouldn’t meet the requirements for submission to PDB-Dev.
Once again thanks for HADDOCK - the tutorials that your team provides really are excellent!
The current version allows to download mmCIF files for the coordinates or coordinates + restraints.
It does contains already quite some information.
The new beta deposition interface should be able to take it as starting point.
Ideally in the future we would like to export all clusters and their stats into one mmCIF.
That sounds great. Thanks again for your help and advice - it is much appreciated
sorry just to circle back to this… where are tehese files found in the haddock2.4 result page or the run folders?
ah i see you can download individual models, thank you