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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: 

restrain multiple portions of proteins with MinMover

Category: 
Design

Hi,

I want to restrain certain portions of my protein when doing cryo-EM modeling.

I was trying to modify the MinMover section of my XML file from

<MinMover name=cenmin scorefxn=cen type=lbfgs_armijo_nonmonotone
        max_iter=value tolerance=value bb=1 chi=1 jump=ALL/>

 to:

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: 

sequence_tolerance is very slow when -ms:num_packs > 1

Category: 
Design

Hi,

here is the command I used. When I set num_packs to 1 which is the default value, the program runs pretty fast, when I set it to other values, the program is stuck there. The version is rosetta 3.6.

 

Post Situation: 

HBNetStapleInterface

Category: 
Design

Hello,

is HBNetStapleInterface avaliable in the current version of Rosetta?

In 2016_15 build i get:

Error: ERROR: Exception caught by rosetta_scripts application:HBNetStapleInterface is not known to the MoverFactory. Was it registered via a MoverRegistrator in one of the init.cc files (devel/init.cc or protocols/init.cc)?

Best wishes,

Staszek

 

 

Post Situation: 

Is the packer aware of non canonical amino acids?

Category: 
Design

I am having a problem when setting the packer to design residues that are non canonical in the pdb file I provide. I have an example for 2ovq where the short peptide called chain C has two phosphorylated residues (TPO at 380 and SEP at 384). When I make a resfile like this:

NATAA
start
384 C ALLAA

Post Situation: 

"Illegal Instruction" for particular Movers/Filters

Category: 
Design

Hi everyone,

I'm attempting to use a script involving a number of different components, but have run into a certain issue.

When I intiate the mover using the attached XML file "design.txt" (which is renamed design.xml when running the script), I get an error of:

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PackRotamersMover - pack=======================
Illegal instruction

The full log is attached (designerr.log).

Post Situation: 

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