Design

I am new to Rosetta. And we hope to redesign a protein and let it easier to dock with another two protiens.  Hope to verify if my approach is correct here.

Step 1) I applied the Rosetta protocol - remodel and create the blueprint file by "~/rosetta/main/tools/remodel/getBluePrintFromCoords.pl"

Step 2) Edit the blueprint file and apply the commands ALLAAxc to all residues. 

Hello, friends,

I was designing the "interface" (possible contacts) of a fusion protein using FastDesign. Since I was running the appliction on a laptop, so far only 200 designed models have been genrated.

I then went on to analyze the result anyway and tried to plot Score VS caRMSD (as shown in the attached file). Here are my questions:

I want to design peptides, allowing redesign and side-chain packing, but no backbone changes. So far I'm using PackRotamersMover, but I would like to write my packer with fixbb instead to have more control.

My question basically is: why do the two following snippets of code not do the same? And what have I missed about PackRotamersMover in my version?

code 1:

Hello

I've tried to design some miniproteins, by following up "Baker lab 2020, science" paper. 

I want to use Rifgen in Rifdock to make disembodied amino acid contact.

But I don't know what flags to start.

They said the initial job of rifgen will take a long time.

On the Rifdock tutorial page, they said "to contact somebody doing some similar jobs and use their flag as a starting point"

So can somebody share your flags?