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Symmetry

Symmetry mode in Remodel for N-terminal extension

Category: 
Design
Loop Modeling
Symmetry

Hello, 

I am trying to use Remodel for N-terminal extension of my homotetramer. I am passing in a single subunit (chain A) and symmetry file (4 subunits identified) with my blueprint with the extra residues of interest. I am getting the following error: 

File: src/protocols/loops/loops_main.cc:253
[ ERROR ] UtilityExitException
ERROR: Can't build a fold tree from a loop with an unspecified cut point.

Post Situation: 

RosettaScripts LinkResidues

Category: 
Design
Symmetry

Hey,

I want to redesign the interface of two three-fold symmetrical proteins and I thought of using RosettaScripts.
I first wanted to make it work on one three-fold symmetrical protein and then continue with the interaction, but I am stumbling on some errors.

I'm using LinkResidues, because the protein is three-fold symmetrical, so a mutation on residue a should also occur on residue b and c, thus without breaking the symmetry of those residues.

I'm using:

Post Situation: 

how to generate the whole molecule that contains all the symmetric chains

Category: 
Symmetry

Dear all,

I have a pdb file which contains three chains (A, B, and C) for a protein molecule. According to my knowledge, the protein should be 3-fold symetric and a trimer of the three chains. Is there a way to generate the pdb file which contains all the 9 chains for the whole molecules?  I can only find some infomation from the original pdb file about the symmetry like these:

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optimisation of a protein-protein interface

Category: 
Design
Scoring
Symmetry

Dear Rosetta users,

I have a symmetrical homo-dimeric structure for which I would like to select a single point mutation that will increase the affinity between the monomers. I thought about design&relax protocol, in which one position is designed while the remaining ones are only allowed to repack. Such a protocol would be used to scan all the interface positions.

My questions is how to set up this in Rosetta Scripts? Perhaps there are easier/better ways to do this?

Thanks for help! Staszek

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mr_protocols with symmetry and ligand

Category: 
Symmetry

Hello,

I have been trying to use mr_protocols on a homologous pdb into a cryo-em density. When I run the protocol with symmetry and without the ligand it works properly. The trouble comes when I try to include a ligand. The resulting pdb is does not contain the ligand. This is the mr_protocol that I have submitted:

#####################################################

#!/bin/bash

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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!

Post Situation: 

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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