I am new to denovo modelling so your help will be greatly appreciated.
I have a density map for a coat protein dimer of a virus (no previous structure of same or similar virus is known so homology is not an option). The two chains seem to swap domain so i cannot segment the dimer further. Rosetta seems incapable to handling a dimer for denovo modelling (each chain is 410 AA long) so i used phenix.map_to_model to get a partial map.
How do i use this partial map to invoke RosettaCM for homology modelling to get a complete model ? How should i generate the alignment file when there are two chains of the same sequence but phenix has build (very) slightly different region of each of the dimers
Thanks in advance, Aseem