I am trying to fix the clashes in a homology model structure I have created of a membrane protein. I tried fixbb to fix only the sidechains, yet I still get clashes ):. Therefore, I want to try to use the relax application in rosetta3.1 to remove clashes. My questions are:
1. Is it O.K to use relax for a membrane protein? If so, what flags should I use to indicate in relax that I want the calculations done on a membrane protein (for instance, would adding -score:patch no_solvation be enough?)
2. How can I make sure that my final result will be clashes free yet not so far structurally from the original input structure?