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Design with limited number of aminoacids at given position

Category: 
Design
Constraints

Hi!

What is the easiest way to allow only a single residue type (e.g. Trp) at a given position during the design?

I use FastDesign Mover with symmetry. I thought about ReadResfile and PIKAA command, but perhaps it could be done directly from the Rosetta Script? Via task_operations=... ?

Best wishes,

Staszek

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Ddg_monomer: implementing disulfides

Category: 
Design

I've been using the ddg_monomer application with high resolution protocol flags and the alternative mutation file format (to obtain more than one mutation) on the constant domain of a TCR (alpha and beta chain).

 

I'm interested in 3 ddg values:

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Symmetric design with PyRosetta

Category: 
Design

Hello,

 

Is it possible to do symmetric design with PyRosetta4 ?

 

I try to pass a symmetry flag to the command line and run pack_rotamers but I get a warning saying that I try to

use a symmetric score function on a non symmetric protocol or something like that.

 

In previous Rosetta versions, there was a symmetric_pack_rotamers, but this method disappeared and there is some symmetry code in

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Should FastRelax be commented out in Calculate_protein_protein_ddg demo?

Category: 
Design

Here's the source code of mutation_script.xml, part of the demo calculate_protein_protein_ddg included in Rosetta (see https://www.rosettacommons.org/demos/latest/public/calculate_protein_protein_ddg/README). I deleted the comments to make it shorter:

 

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RosettaMatch outputs

Category: 
Design
Enzyme Design

I've been running several rounds of RosettaMatch lately and I'd like them to go faster. I'm pretty sure writing matches is the part slowing it down. Is there anyway to limit the number of matches it outputs? For example, for the same matched sequence (say H133H135H432), I get anywhere from 50-400 cloudPDB files. I don't want more than the first one or two, because the rest are almost always just different ligand positions and I'll end up running EnzDesign anyways. I'm using these flags:

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How to transform a pose from symmetric into non-symmetric?

Category: 
Design
Scoring
Constraints
Symmetry

Hello,

Is there a way to break the symmtery of a pose in the middle of a Rosetta script? I want to avoid writing the PDBs and feeding them again to a new script.

Any suggestion is highly appreciated!

Thanks!

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symmetric design in the presence of a nonsymmetric ligand

Category: 
Design
Symmetry
Small Molecules

Hello,

I am trying to design a C3 symmetrical protein with a ligand bound at the C3 interface. What is the best way around this in RosettaScripts? I was thinking to first symmetrize the pose with SetupForSymmetry and then add the ligand with AddChain mover. But it seams, SetupForSymmetry is not compatible with extra_res. As soon as the script arrives at SetupForSymmetry, it throws the following error:

Post Situation: 

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