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How to minimize the decoys obtained from backrub?

Submitted by Vedasheersh on Wed, 2017-06-14 10:26
Category: 
Design

Hello there!

I am trying to design a protein using backrub application. I have two questions.

1. Is nstruct 100 enough to sample such a problem? (I am only trying to design 15-20 out of 560 amino acids)

2. From the output of backrub, what is the best way to minimize the decoys to score them so that I can compare with the wild type?

Thank you

Veda

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Rosetta 3 - Applications

Model two domain protein

Submitted by sn on Sat, 2017-05-06 13:21
Category: 
Design

Hi,

I want to model a protein that has two domains. I have two separate domains modeled using Rosetta. I want to merge these two domains based on the cst file that gives inter domain distance constraints.

What are some of the best ways to model it? These domains are  asymmetric. Can I use RosettaCM to do the modeling? Or should it be more like fold and dock?

 

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Rosetta 3 - Applications

optimisation of a protein-protein interface

Submitted by sdh_h on Thu, 2017-05-04 05:06
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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Rosetta 3 - General

Fast relax not working

Submitted by eyong123 on Fri, 2017-04-21 06:06
Category: 
Design

Hi I have not used Rosetta for a while.  i wanted to relax my receptor for enzyme design and i kept on having the message

Evaluation Creator active ... 

protocols.relax.FastRelax: WARNING: Pose has no residues. Doing a FastRelax would be pointless. Skipping.

protocols.jd2.JobDistributor: S_0001 reported success in 0 seconds

protocols.jd2.JobDistributor: no more batches to process... 

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs att

here is my flag file

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Rosetta 3 - Applications

Error using InterfaceHoles filter

Submitted by SenyorDrew on Fri, 2017-04-14 08:55
Category: 
Design

Hi,
I'm trying to use the InterfaceHoles filter and get the following error:

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER holes=======================
core.scoring.packing.compute_holes_score: compute_holes_surfs try: 1
sh: 1: alpha20_surf: not found

Any idea where alpha20_surf needs to be (or if it needs to be compiled?)

 

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Rosetta 3 - General

cxx11 error with antibody modelling

Submitted by bogac on Wed, 2017-03-08 09:14
Category: 
Structure prediction
Design

Dear all,

I built the last release 2017.08 recently. I have not encountered any error during the build. Here is the command I ran: 

./scons.py -j8 mode=release bin extras=cxx11 extras=mpi

I have gcc version 5.4.0 so according to build tutorial this should new enough to have C++11 support. 

But when I am running antibody.linuxrelease as according to the protocol on

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Rosetta 3 - Build/Install

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