having now had a look at PyRosetta I’m still not sure this is possible.
If I want to use fragments and CCD my understanding is that you need to convert to a centroid model and then back to full atom for High-Res refinement. Unfortunately I don’t think centroid mode understands DNA residue types (at least when I have tried).
So I am able to load my complex and run high-res refinement on my model successfully (I think) but I would really like to do some more aggressive frag set moves beforehand.
Is there any way around this?
P.S. I should point out that my complex is quite large so I have not idealized my models.