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Ddg_monomer: implementing disulfides

Submitted by kabol on Wed, 2016-11-30 02:39
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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Rosetta 3 - Applications

Symmetric design with PyRosetta

Submitted by dsim on Thu, 2016-11-17 07:50
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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PyRosetta - General

Should FastRelax be commented out in Calculate_protein_protein_ddg demo?

Submitted by cossio on Mon, 2016-10-31 12:01
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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Rosetta 3 - Applications

RosettaMatch outputs

Submitted by mwfranklin on Tue, 2016-10-11 11:46
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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Rosetta 3 - Applications

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

Submitted by msardejani on Tue, 2016-10-04 16:55
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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Rosetta 3 - General

symmetric design in the presence of a nonsymmetric ligand

Submitted by msardejani on Fri, 2016-09-30 15:17
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:

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Rosetta 3 - Applications

restrain multiple portions of proteins with MinMover

Submitted by Karol on Wed, 2016-09-07 08:29
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:

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Rosetta 3 - General

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