Design

I would like to run a design protocol on a protein that has, as its asymmetric unit, 2 proteins with an ion. I have done some purely AA-based symmetric design before with 2 chains controlled by separate virtual jumps and my own python-generated symdef file but I'd rather avoid doing that again :-) 

My hope was that I could put (even if suboptimal) the 2 chains and the ion in a single chain and proceed as usual in symmetric design with one chain.

Dear Sir and Madam,

When I run such a script "~/rosetta_src_2020.08.61146_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol Design.xml -s some_relaxed_protein.pdb -database ~/rosetta_src_2020.08.61146_bundle/main/database/ -restore_talaris_behavior true -remodel:use_pose_relax true -score:set_weights pro_close 0 cart_bonded 0.5 -nstruct 10 -out:prefix design_" for insertion one amino acid, replacement one original amino acid into another and building additional disulphide I meet with the following error:

"[FILE]: SIGSEGV

Dear all,

I am trying to use Rosetta dock and antibody design modules to design antibody in order to improve the affinity of the antibody to the antigen.  Firstly I docked the antibody to the antigen. In this step I got 500 and antibody-antigen complex models and selected top 10 models based on the lowest I_sc energy. Then I ran AntibodyDesign using a command like the follow for each of the 10 complex models:

Hi All,

I came across the Coupled Moves protocol recently and it sounds like an interesting alternative to FastDesign that I've been predominantly using. I tried to implement the CoupledMoves Mover within my RosettaScripts design script, however, I keep coming across the following error:

ERROR: FoldTree:: residue_edge is undefined for root vertex
ERROR:: Exit from: src/core/kinematics/FoldTree.cc line: 2317
[0m[0mprotocols.rosetta_scripts.ParsedProtocol: [0m[31m[1m[ ERROR ][0m Exception while processing procotol: