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Hi, I have some questions on protein design using Rosetta, specifically on the coverage of sequence space.

Hello

I want to repair my missing residues by loop modeling. As it has shown In the demos and tutorial, I should have a file like x_missing_loop.pdb

it is like main pdb file of target protein BUT it hase something called table energy pose bellow it. How I should make this table energy pose. ???? tutorial has not said anything about making this table energy pose

I have attached that input file from demos, please explain how I can make table pose energy which is under cordinations data?

 I  read the paper Rosetta and the Design of Ligand Binding Sites doi:10.1007/978-1-4939-3569-7_4.

then try to use  EnzRepackMinimize  to design the protein.

But FavorNativeResidue was set as 0.5-3.0, the mutant position numbers are same and there are too many mutant positions.

However, I use the PackRotamersMover  by changing  FavorNativeResidue and can get different mutant position numbers.

How can I solve it? Thanks.

Hi I'm running csRosettaCM with POMONA alignments and I would like to include NOE constraints in my models. Some of my constraints are on the side chains, therefore I cannot implement them in centroid mode, and would like to implement them in the full atom mode. However, it seemed like csRosetta has ignored my cst_fa_file and did not take in the constraints on the side chain. Any suggestion on how to fix this? And if it is possible to run csRosetta in full atom mode directly?

I have the following in my flags file:

-cst_fa_file noe_fa.cst