I am currently trying to set up a docking run between two proteins that have compatible symmetry, and almost certainly interact along a 3-fold symmetry axis. One molecule is trimeric, the other is a D3 hexamer, with protomeric MWs of 20 and 25 kDa respectively. I have experimental (x-ray) structures for both proteins, and an initial model where the two proteins are in contact, and lined up with the 3-fold axis of each along Z. I therefore want to search only rotations around Z, along with a small Z-translation shift. The question is how to do this – the docking documentation doesn’t address this point. On a related note, 1) how does one constrain side chains that are remote from the expected interaction site and 2) how finely should the angle and translation increments realistically be sampled. I ask this because the proteins are relatively large, and I will be using a desktop machine for the calculations.
Any help appreciated. I am new to Rosetta and am not a Python programmer, so clarity is valued.