I'm having trouble re-designing a 2-component symmetric nanoparticle with small gaps along lines that connect symmetry axes. The starting pdb looked good, so I selected 2 chains that define the unit cell and apply a symmetry file to enable the computational savings associated with symmetry. However, the symmetric docking step that's triggered by the rosetta.protocols.symmetry.SetupForSymmetryMover method seems to smush the chains together, resulting in a smaller radius nanoparticle with VdW clashes.
I've tried a few things but nothing's worked so far. I tried to start from the assembled structure and supply the symmetry info directly using:
sd = pyrosetta.rosetta.core.conformation.symmetry.SymmData()
I also tried to figure out how to replace the atom tree of the symmetric pose with the positions from the original pose, but couldn't figure out how to do this from the documentation. Does anyone know of a workaround that I could use for this issue?
Thanks, any help would be greatly appreciated!