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Design

Did RosettaScripts recently switch to fully parallel MPI?

Category: 
Structure prediction
Design

Hi, trying to figure out if something isn't working properly or if it's working as intended and I missed it. I was using the Topology Broker via Rosetta Scripts from the 2016/Week 46 build of Rosetta and when I ran my script via MPI, it would create one nstruct per core, not including the controlling core. I was able to see this in the log; different commands were marked with (0), (1), (2) etc, for presumably which core the message came from. So if my command was: 

mpiexec -np 4 rosetta_scripts @flags -nstruct 10

Post Situation: 

conformational sampling of multi domain protein

Category: 
Design

Hi all

       I have a protein with two doamin connected with two linker. the crystal structure shows only closed conformation. I don't know the open conformation and want to sample it. so I want to only change the conformation of linker region treating the two domain as rigid. is there any protocol available on rosetta that I can use for this purpose? Sorry if I haven't put my question in a very clear way. I am new to rosetta and not well aware of most of the terminology used here.

 

Thank you

Dhiraj 

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PyRosetta FastDesign

Category: 
Design

Dear Community,

 

I have been trying to implement FastDesign in PyRosetta. This is my code so far, I could not find documentation or examples to help me get the code running:

 

x = FastDesign()
x.apply(pose)

 

I get the folloing error:

Segmentation fault (core dumped)

 

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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.

 

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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

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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

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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

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