Model monomer to fit cryo density map of a filament

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- December 13, 2018 at 2:58 am #3056
  Anonymous
  Dear all,
  
  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!
- December 19, 2018 at 5:58 pm #14548
  Anonymous
  Hello,
  
  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.
  
  -Frank
  - December 31, 2018 at 12:49 am #14549
    Anonymous
    Dear Frank,
    
    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:
    
    make_symmdef_file.pl -m HELIX -p monomer.pdb -a A -b B:2.25 > helix.symm
    
    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?
    
    -Buddy
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