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!
It sounds like you already have a model for the monomer. If so, the best strategy is to use Symmetric Docking with the fit-to-density term enabled.
Thank you for your suggestions! I do have a question about symmetric docking. To use symmetry docking, symmetric file is required. Based on the documentation, I should use the -HELIX option. I want to use the following command:
However, I only have monomer pdb and only one chain (Chain A) and no chain B. I am wondering how do I define the helical symmetry in this case?