I want to extend an N terminal helix in my protein while maintaining the helical structure. however the structure of my protein is such that the newly modeled residues will be in close proximity to rest of the protein. So rosetta remodel should choose the residues considering how well it will pack against rest of the protein. however the visual inspection of the final model suggests that it has not choosen the correct residues. for example, it has modeled a non polar residue close to a charged patch. it has also selected 2 contiguous glycine residue to build the helix.
what is the best way / rosetta protocol to use for this purpose?