I am trying to learn Rosetta myself and I have a question regarding abinitio structure prediction. I have a poor resolution cryo-EM map (~20 A) of a filament and I want to model the monomer to fit the density map. I have ~200 aa squence of my monomer, which is a truncated product of ~400 aa protein. I have the structure of the 400 aa protein and I want to know how I could model the 200 aa monomer under the guidance of the EM map. I was reading the manual on EM modeling module and I am wondering should I just use the -edensity flag? What is the common strategy when comes to monomer prediction of a filament?
Thank you for your help!