Thanks for your reply.
I have been folding membrane proteins and soluble proteins in Rosetta 3.1 for a while. But I want to move on to incorporate some experimental data during folding. According to my understanding, simply changing the score function wouldn’t help. There is a multilayer membrane environment designed to do this job in regular Rosetta release 3.X. What I really need is to have some flexibility in pyRosetta, that would allow me to vary the membrane environment and refine structure with some data. Homology may help. But it will be great, if I can do this in PyRosetta with more flexibility.