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Minimizing a Symmetric Structure

Submitted by ammar.x.gilani on Wed, 2023-08-02 11:10
Category: 
Symmetry

Hi, I have a structure with two chains (1 and 2 ) which are identical. My goal is to minimize its structure using FastRelax with a symmetry constraint.

Creating symmetry file: 

make_symmdef_file.pl -p Data/2mcg.pdb -a 1 -i 2 > Data/2mcg.symm

Structure minimization:

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PyRosetta - General

Symmetry definition question

Submitted by mrconde96 on Sun, 2022-10-02 05:34
Category: 
Symmetry

Hello!

I'm relatively new to Rosetta and I'm trying to apply symmetry in the BlueprintBDR. As I only know that I want C3 symmetry I used the general symmdef file for this symmetry. Still, I noticed that it just rotates the subunits with no translation from the COM of the arrangement, which leads to an overlap in residue coordinates, which in turn leads to problems in the minimization protocol. I have attached a picture of an example of what I got and the symmdef file used to obtain it.

Any help is greatly appreciated!

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Rosetta 3 - Applications

Symmetry breaks due to small structure gaps

Submitted by dbiedermann on Mon, 2021-09-20 17:39
Category: 
Symmetry

Hi everyone,

I'm having trouble re-designing a 2-component symmetric nanoparticle with small gaps along lines that connect symmetry axes. The starting pdb looked good, so I selected 2 chains that define the unit cell and apply a symmetry file to enable the computational savings associated with symmetry. However, the symmetric docking step that's triggered by the rosetta.protocols.symmetry.SetupForSymmetryMover method seems to smush the chains together, resulting in a smaller radius nanoparticle with VdW clashes.

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PyRosetta - General

calcium metal nomenclature: Rosetta_cm confusing HETATM CA (calcium) with ATOM CA (alpha-carbon)

Submitted by rlwoltz on Tue, 2021-08-03 23:26
Category: 
Structure prediction
Constraints
Symmetry
Membrane

Dear community,

I had this posted under a different sub-forum but I realized it didn't fit that forum so deleted it and reposting here.

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Rosetta 3 - General

MPI optimization on TACC stampede2 HPC

Submitted by rlwoltz on Tue, 2021-03-16 18:07
Category: 
Structure prediction
Loop Modeling
Symmetry
Membrane

Dear community,

I am new to MPI so please correct any misuse of terms. My question is about optimizing for MPI on an HPC or a second (preferred) solution to my issue is to optimize my RAM usage so I don't have to run MPI, serial would actually improve overall models produced anyways.

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Rosetta 3 - General

Metal Ion in symmetric design

Submitted by tschiex on Wed, 2020-07-08 05:28
Category: 
Design
Symmetry

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.

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Rosetta 3 - Applications

Structure refinement for helical assembles using Rosetta

Submitted by xiaoyanzi on Thu, 2020-06-18 00:34
Category: 
Symmetry
Hi all, I'm very new using Rosetta to make structure refinement. I'v read lots of related articles and also read the Tutorial: Rosetta tools for structure determination in cryoEM density. But I still not sure how to start my first Rosetta try.
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