I'm new to Rosetta and I'm not sure if it is feasible for solving my problem. I have an octameric complex consisting of eight short (20 amino acid) helices packed together. The peptide exists in two conformations in the complex - say A and B. This means that the asymmetric unit is made up of an 'AB' dimer. Could anyone tell me if having more than one chain as the asymmetric unit will be a problem with defining the symmetry or docking? When generating the symmetry definition file with make_symmdef_file_denovo.py would I specify the number of subunits as 4 (as I have four asymmetric units) or 8 (since there are 8 subunits)?
As I believe I have two possible symmetry types (c4 and d2) is it reasonable to assume I should just try both and then evaluate which is correct based on the lowest energy structures?
Finally, as I know each subunit is an alpha helix I'm not sure if the docking protocol starting with a canonical alpha helix monomer structure, or fold-and-dock is more suitable. Can I restrict only the backbone residues in order to maintain the helical structure but allow flexibility in the side chains.