Hi Mary,
I was wondering when you would want to change multi_body_factor= 1? Is this something you would change when you have multiple rigid body domains? From the name, that's what I'm guessing it's for. I'm refining a large over 400 kD multimer complex with two complexes in the ASU. So, if I have 5 chains in each multimer would I want to try to change the multi_body_factor to 10? Or does multi_body_factor affect something else.
Short answer: you would never want to change multi_body_factor. It was introduced while systematically searching for the best parameterization of the automatic multiple-zones protocol for rigid body refinement. I'll go through and change the expert_level for this and similar parameters, so you won't normally see them in the GUI. Ralf