I'm working on a Protein-DNA interface, but I'm having some trouble with PyRosetta. I have a PDB file with the protein bound to DNA, from x-ray crystallography data to start from, and I need to refine the interface binding. Eventually, I'd like to modify the DNA sequence found in the PDB and investigate binding of known mutants.
Based on D110_DNA_Interface.py demo script, I'm using the DockMCMProtocol for full atom docking. However, as binding takes place in a known domain of the protein, I'd like to restrict sidechain packing to a portion of the sequence. DockMCMProtocol.set_move_map() suggests that this is possible, but I get a segmentation fault when it's used. A MinMover using the same move map works as expected. Has anyone had a similar experience, or know a work around?
Additionally, is DockMCMProtocol the best way to perform protein-DNA docking? Auto-complete for 'Dock' in iPython brings up a lot of items, and I've noticed that some of the demos/tutorials are a bit out of date. Are there any resources that give an overview of what steps a particular Mover actually performs?
Thanks in advance!