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I found a structure of a binary protein complex and tried to use it as my template to predict the combined structure of another 2 proteins. In this case, should I use the protein-protein docking protocol or the comparative modeling protocol?  If I should use the protein-protein docking protocol, is there anyway for me to utilize the PDB file of the template structure to save me some work? And if I should use comparative modeling, how can I build a structure by inputting 2 queries? I assumed that homology modeling only deals with one input query?

Using antibody_designer to graft loops on one CDR. I'd like to fix the sequence of the grafted loop to native. It appears to ignore the 

I have tried something like this in my cdr_instruction file

H3 GraftDesign ALLOW

ALL SeqDesign FIX

 I've also tried passing it a resfile forcing everything to be native like so

NATAA

start

Hi, I am using Rosetta 3.7 and the following flags for relax:

relax.linuxgccrelease -s complex.pdb -out:suffix _relax -nstruct 5 -relax:default_repeats 5 -out:path:pdb ./ -out:path:score ./ -ignore_unrecognized_res

I was wondering if there are any default restraints on backbone displacement in this, I believe in principle unconstrained, procedure.

With thanks and best regards,

Szymon

I have been using Rosetta design for quite a while but I did not pay attention to what Resfile header would do. I looked for descriptions and examples files different people have shared and used and I am unable to understand when I should specify NATRO or NATAA in the header?

I want to perform different tasks. For example:

1) Mutate specific residue to ALLAA and I use header like:

NATRO
start
30 H ALLAA

whereas, I found someone using following header: