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PyRosetta

Mistake about rosetta.init()

Category: 
PyRosetta

Dear All:

I have a mistake about rosetta.init() as 'AttributeError:'module' object has no attribute 'init''.

From rosetta import * ; from pyrosetta import * and pyrosetta.init() are all fine. My os is ubuntu 16.04.  Pyrosetta is 'PyRosetta4.Release.python27.ubuntu.release-151.tar.bz2'.

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Problem about Pyrosetta installation win7

Category: 
PyRosetta

I have installed the Pyrosetta 4 (win vision) on my win7. I can do the command of "from rosetta import *", but when I do "from pyrosetta import *", there are mistake "ImportError:No module named pyrosetta". What can I do for that?

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Fragment Quality

Category: 
PyRosetta

Dear All,

 

I am trying to measure the quality of the 9-mer fragment file in order to debug the Abinitio fold of a structure I have designed. I am trying to do it in PyRosetta.

 

This is my script so far:

#Choose Fragment
fragset = ConstantLengthFragSet(9)
fragset.read_fragment_file('9-mer')

#Setup Calculator
calc = FragQualCalculator(fragset , 1.0 , 30.0)

Am I in the right track?

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How To Read PyRosetta Documentation - GenericMonteCarloMover as example

Category: 
PyRosetta

Dear All,

Is it possible to explain how to read these PyRosetta documents? it seems they show what each function takes, but it is not clear what are these arguments specifically and where to get them from.
URL: http://graylab.jhu.edu/PyRosetta.documentation/rosetta.protocols.simple_moves.html#GenericMonteCarloMover-apply

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SASA of pose

Category: 
PyRosetta

Dear All,

 

Is there a way to isolate or select the different structure layers from the pose according to their SASA (surface accessable surface area) in PyRosetta?

 

I have a python script that can do this from a .pdb file, but is there a way to do it from a PyRosetta pose?

 

I read that there are movers called LayerSelector and SelectBySASA both in Rosetta for Rosetta Script, is there their equivilent in PyRosetta?

 

Thank you

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generate_nonstandard_residue_set Exception

Category: 
PyRosetta

generate_nonstandard_residue_set is giving me an error I don't understand. Can anyone tell what I'm doing wrong here?

In [2]: %paste
from rosetta import *
from pyrosetta import *
init()
params_paths = utility.vector1_string()
params_paths.extend(["GUA.params"])

In [3]: nonstandard_residue_set = generate_nonstandard_residue_set( params_paths )
---------------------------------------------------------------------------

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Cutout part of a protein

Category: 
PyRosetta

Hello People,

 

I am trying to find a way to cut out part of a protein and save to a new .pdb file.

 

So i have a protein and i want to cut out a section (from amino acid 315 to 330 for example), and save that cut out (and maintain the original 3D structure) into a new .pdb file.

 

I tried searching if there is a built-in PyRosetta function/method that does this, or if there is a script that does this, but i could not find.

 

Anyone can help me or guide me?

 

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