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RosettaHoles for PyRosetta - Void Detection/Scoring

Category: 
Design

Dear All,

 

Is there a mover in PyRosetta for scoring/detecting/desining a protein's core especially getting rid of voids?

 

I understand there was a RosettaHoles, which i cannot find in Rosetta 3.8 (where did it go)? Nor any info about it and how to use it, or its .cc file so i can try and write something similar in python.

 

I tried RosettaVIP in C++, but i could not get it to work properly (get rid of voids), nor could i find something similar in PyRosetta.

 

Post Situation: 

domain:domain fusion

Category: 
Design
Loop Modeling

Dear all

I would like to insert a domain at the N-terminus of protein and at the same time build different linker sizes. Which application is the best suited? My impression is that domain insertion protocols, like remodel, broker or AnchoredPDBcreator, assumes that we are not at the end or a protein. Is there a way to do this?

thanks in advance

best

felipet

Post Situation: 

How to minimize the decoys obtained from backrub?

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

Post Situation: 

Model two domain protein

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?

 

Post Situation: 

optimisation of a protein-protein interface

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

Post Situation: 

Fast relax not working

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

Post Situation: 

Error using InterfaceHoles filter

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?)

 

Post Situation: 

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