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CoupledMoves not altering backbone coordinates?

Category: 
Design

HI All,

I'm beginning to play around with CoupledMoves for flexible backbone design and I am unable to get it to alter the protein backbone coniguration.

When I run the tutorial here (https://github.com/Kortemme-Lab/coupled_moves-tutorial) it works. But when I try and apply that (or similar) command to another protein it will deisgn the sequence, but all the output pdbs have no coordinate changes. 

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De novo backbone trace from fragments

Category: 
Structure prediction
Design
Loop Modeling

Dear Rosetta experts,

I have been using rosetta mainly for refinement and iterative local rebuilding into cryo-em densities at reolustions of ~3-3.5 Angstrom. I am wondering how (or if it is possible) to combine and complete a set of backbone fragments predicted by external software into a single backbone trace using rosetta. To make matters somewhat more complicated I would need to do this without any sequence information using only polyA fragments.

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RosettaScripts filter BuriedUnsatHbonds2 missing still

Category: 
Design

Hello, 

Can the BuriedUnsatHbonds2 filter be pushed to release? It gets called in a rosetta scripts xml included in the supplementary materials for this paper (published in 2017): DOI: 10.1126/science.aan0693

 

Thanks!

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symmetric design w/ hbnet and unsatisfied_buried_penalty score terms

Category: 
Design

Hi All,

I am working on designing some symmetric structures and am currently using REF2015 + hbnet. In addition, I want to add the buried_unsatisfied_penalty. When I add this term to the score function, it works and can score 'non-symmetrized' structures just fine. However, when I try to score a structure that has been 'symmetrized' I get the following error: 

File: /home/benchmark/rosetta/source/src/core/pack/guidance_scoreterms/buried_unsat_penalty/graph/BuriedUnsatPenaltyGraph.cc:637

[ ERROR ] UtilityExitException

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Can I believe the antibody design result?

Category: 
Design

I am trying to do antibody design with the  RosettaAntibodyDesign, but some of my colleagues told me that they fell to obtain successful designers with the  RosettaAntibodyDesign (RAbD). They ran the RosettaAntibodyDesign on the crystal structure of an ab-ag complex with a dG_seperate of about -20 REU, and got some designers with dG_seperate of about -40 REU. However, they did experiments including ELISA and SPR and found that these antibody designers did not bind to the antigen at all!

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How to use MHC Epitope energy (mhc_epitope) to deimmunize a protein structure?

Category: 
Design

Dear all,

The MHC Epitope energy (mhc_epitope) alogrithm  (https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/MHCEpitopeEnergy) is for deimmunization of epitopes. However I cannot understand how to use it. 

I used the pdb file 2b3p.pdb and the score controlling script in the introduction webpage as the inputs and run the following command:

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core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard

Category: 
Design

Dear developers,  

I tried to follow the antibody design protocol from the Nature protocol articles but unfortunately I keep getting the following error when I try it:

core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard

This is my command line: 

antibody.default.linuxgccrelease -ignore_unrecognized_res -fasta antibody_chains.fasta

and this is the content of  ROSETTA_CRASH.log:

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