I have a Cryo-EM density and AA sequence for a protein , but the density is not good enough for assign the residues unambiguously.
I'm particularly interested in one alpha-helix and based on secondary structure prediction, I have roughly known the AA sequence for the helix.
But the secondary structure prediction can't tell the boundary of the helix unambiguously.
Could anybody have any ideas about how I can get the correct register for the helix using Rosetta???
I'd like to try to thread all possible registers onto manually-build poly-A alpha-helix model and run rosettaCM to refine each threaded model. I'm wondering if RosettaCM is a resonable method to do this as the helix is only 20-AA long and for each model it's fully threaded.
Can I just try fastRelax for each threaded model and select the best one?
Thanks a lot,