Just a quick post to ask for advice: I have a protein that I need to dock to a ribosome (or pieces of it). Does the new haddock now handle mmcif files?
Better to convert to PDB format for submission.
If not, I can split the ribosome into thepieces I need, however, I do need the long rRNA (otherwise too much volume that is occupied looks as if it is available).
How would you suggest docking a protein to a protein-RNA complex? Do I just add a lot of unambiguous distance restraints to keep the RNA in place, or there is a way to have protein/RNA in the same docking block?
You can input a protein-RNA complex as one molecule (as long as they have the same chainID and no overlapping numbering). And even define it as rigid if you want.
Alternatively you could input the various molecules separately and use to option to fix them at their origin (for those forming the protein/RNA complex onto which you want to dock your other protein).
Depending on the size of your system you could consider using coarse-graining.
And all this of course in our new 2.4 web portal.