Model monomer to fit cryo density map of a filament

[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!

[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

[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

[Author]

Posts