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This element is not expected.

Submitted by ac.research on Fri, 2017-10-13 03:47
Category: 
Design

I am trying to replicate the work of the paper: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature23912.html?foxtrotcallback=true

It seems the Rosetta Script in the supplimentary meterials is old because when I try to use it I get a lot of typo errors, anyway I changed it but I could not find a way to fix this error:

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Rosetta 3 - General

Allow region of protein to move in a certain direction

Submitted by sn on Wed, 2017-08-23 17:07
Category: 
Design

Hi,

I have a protein structure. I want to move a specified region (say residues x to y) of this protein in a any direction (more like a dynamic simulation). Is there a protocol that allows this in Rosetta? I have tried the backrub, relax with constraints.

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Rosetta 3 - Applications

Muting output in pyrosetta

Submitted by SenyorDrew on Mon, 2017-08-14 08:13
Category: 
Design

Hi,

I have a function in pyrosetta that performs repack, and I call this function many times.   Right now I get tracer output from core.pack.task:

e.g.

core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 143 rotamers at 8 positions.

Is there a way to mute this output ONLY while in my function? i.e. I'd like to mute this output and then turn it back on later in my script?  

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PyRosetta - General

De novo Protein Design

Submitted by ac.research on Sat, 2017-07-15 10:39
Category: 
Design

Hello All,

 

I am trying to learn how to preform De novo Protein Design.

 

I looked for tutorials and demos but did not find any. Can someone point me to the location or material where i can read about how to preform this protcol? just something basic so i can understand where to start from.

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Rosetta 3 - General

Did RosettaScripts recently switch to fully parallel MPI?

Submitted by beowulfey on Thu, 2017-07-13 09:02
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

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Rosetta 3 - Build/Install

conformational sampling of multi domain protein

Submitted by dhirajks on Tue, 2017-07-04 11:20
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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Rosetta 3 - Applications

PyRosetta FastDesign

Submitted by ac.research on Tue, 2017-07-04 10:23
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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PyRosetta - General

RosettaHoles for PyRosetta - Void Detection/Scoring

Submitted by ac.research on Sat, 2017-07-01 11:28
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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PyRosetta - General

domain:domain fusion

Submitted by felipet on Thu, 2017-06-15 13:13
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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Rosetta 3 - Applications

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