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PyRosetta

PyRosetta init() error (Linux)

Category: 
PyRosetta

Dear all,

I've been trying (and failing) to build PyRosetta (monolith release 95) for a couple of days now.

I'm running Kubuntu 15.10 64bit.

I've tried running PyRosetta with Python 2.6, 2.6.6 and python 2.7 (ipython & regular).

I never get complaints for from rosetta import * or import rosetta, but when I try to init() I get

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Install PyRosetta 101?

Category: 
PyRosetta

Dear Reader!

I'm doing computational redesign as the project for my  bachelor degree and my supervisor told me to use Rosetta/PyRosetta. I've been trying to install this thing on my computer for about three weeks now and I haven't gotten anywhere. Can somebody please explain how to do for a person who never have been programming or used the command tool in the computer before? I have installed it in my PC through a  .exe-file, but when I click on the shortcut nothing happens. 

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ClassicRelax: how to block the backbone

Category: 
PyRosetta

hello! isnt the following command meant to keep the backbone fixed? cos i obtain a model with a RMSD of about 1A from the initial model.

movemap=MoveMap()    
movemap.set_bb(False)
relax=ClassicRelax()
relax.set_scorefxn(scorefxn_tala)
relax.set_movemap(movemap)
relax.apply(sample_pose)

Thanks :)

 

 

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How to determine interface residues

Category: 
Scoring
PyRosetta

Hi,

I have a couple questions about fold-trees and how interfaces are calculated in pyrosetta (or rosetta).  I have a structure of an antibody-antigen that I have prepared using rosetta (attached).  A visual inspection shows that residue B:TYR210 is making a number of close contacts with residues in Chain C (the antigen).  However, when I construct an Interface object in pyrosetta, this residue is not identified as being in the interface (using a cutoff of 5.0A):

 

from rosetta import *

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PyMOL did not work from a remote machine with PyRosetta

Category: 
PyRosetta

Hi all,

I want to show the structures by PyMOL_mover to PyMOL in another computer,so according to the tutorial by setting pymover.link.udp_ip = #IP(where PyMOL is running) and pymover.link.udp_port = 65000,but after pymover.apply(pose),the pymol did't show anything,(if PyRosetta and PyMOL run in the same computer,it works),have anyone met this problem,thanks a lot if you can help me!

Thanks,
Jeremy

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pymover = PyMOL_Mover() hangs IPython?

Category: 
PyRosetta

I followed the instructions here (http://www.pyrosetta.org/pymol_mover-tutorial) to setup the PyMol Mover. But when I try to execute

pymover = PyMOL_Mover()

my IPython session hangs. This statement never finishes execution.

I am using Ubuntu 14.04.1, 64bits, and PyRosetta r48.

Any idea on what's the problem here? I can provide more specs about my system if needed.

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