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Symmetry

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: 

dock & design

Category: 
Docking
Design
Constraints
Symmetry

Dear All,

I would like to simultaneously dock and design two (or more) identical subunits into a a symmetric homooligomer.

Input:

- backbone structure of a monomer (no sidechains!);
- initial arrangement of the subunits;
- constraints that precisely define interactions between the subunits.

Simulation:

Post Situation: 

multiple symmetry definition files

Category: 
Symmetry

Hello,

Multiple input structures are provided as a list (in:file:l) or in a single silent file (in:file:silent).

Is there an easy way to provide also symmetry definition files for the individual structures? (symmetry:symmetry_definition)

Thanks you for suggestions!

Best wishes,

Staszek

 

Post Situation: 

RosettaScripts - SetupNCS mover

Category: 
Design
Constraints
Symmetry

Dear all

I was trying to mix ligand docking with protein design of a symmetric dimer by using the SetupNCS mover. I still don't know why the mover is not being used...the resultant pdbs were modified at the sequence level but both chains are different.

thanks in advance

felipet

 

The script used is:

 

        <MOVERS>

                <SetupNCS name=ncs bb=1 chi=1 symmetric_sequence=1>

Post Situation: 

wallpaper symmetry definition file

Category: 
Symmetry

Hello All

The supporting information of the Science paper by Gonen et al. refers to a perl script for generating wallpaper symmetry definition files. But I cannot find it even in the recent version of Rosetta.

The manuscript points to a file make_Pn_tiling.pl

"It can be found in the Rosetta directory path ‘apps/public/symmetry/make_Pn_tiling.pl’.

I was wondering if may be any of the current users had access to it.

Thanks

Post Situation: 

Symmetry definition for apolar helix

Category: 
Symmetry

Hi,

I am struggling to generate a symmdef file for a helical model and I am hoping someone can help.

The helical parameters are as follows: rise = 17 Angstrom with 4.674 subunits per turn. The helix is apolar i.e. the ends of the helix are the same as related by 180 degree rotation. The repeating unit is a dimer with C2 symmetry. In the attached pdb (ca only to avoid upload limit) the A and B chains form the dimer which is related to the next C/D pair by the helical symmetry I mentioned.

Post Situation: 

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