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PyRosetta

Availability of PyRosetta compiled with Python3.8

Category: 
PyRosetta

Hi,

I have a commercial licence for PyRosetta.  I recently upgraded to Ubuntu20.04, which comes with Python3.8.  I understand that you're planning on releasing PyRosetta compiled with Python3.8 and was wondering when that might be available.  I tried compiling PyRosetta myself (and have been previously sucessful with python3.6 on ubuntu18.04), but ran into issues compiling under stock Ubuntu20.04.

 

Thanks

Post Situation: 

can't install ipython + all tests fail

Category: 
PyRosetta

Hi all,

  I am trying to install ipython to eventually install pyrosetta as instructed by this guide:

http://www.pyrosetta.org/documentation/windows

However, I can't install iphyton (enable to locate package error) 

I tried many solutions that I found online, but all failed to solve it

Moreover, when I try to continue without solving it, all the tests fail. I checked the python version as recommanded here:

Post Situation: 

How to fold-and-dock in PyRosetta?

Category: 
Structure prediction
Docking
Symmetry
PyRosetta

I'd like to do something similar to regular Rosetta fold-and-dock but in PyRosetta.  I've looked at D060_Folding.py and D100_Docking.py examples and while I (mostly) understand what each is doing, I have no idea how to combine them.

How to get a foldtree with symmetry? (in my case it's just simple C3) 

How to combine folding and docking?  Just alternate calls to folding.apply(test_pose) and dock_prot.apply(test_pose)?  (It can't be that simple...)

Post Situation: 

getting .params file for a ligand composed of protein and lipid

Category: 
PyRosetta

Hi all,

 I have a ligand which is composed of protein+lipid and it is a big molecule(please see the attachment). How can I use molfile_to_params.py and get a .params file?  I tried it once, but it gave me several .params and several pdb files as output which I believe it is not right.

I highly appreciate your help.

Post Situation: 

Running pymol mover on windows 10

Category: 
PyRosetta

I am trying to get pymol mover to work in jupyter notebooks along with pyrosetta. I am working on windows 10 using a linux subsystem.

PyRosetta works great. I have installed pymol via anaconda3 and I have files that are a part of pymol that I can see in my terminal. When I run the following

 

from pyrosetta import PyMOLMover
pymol = PyMOLMover()
pymol.apply(pose)

 

Post Situation: 

Relaxation vs minimisation

Category: 
Structure prediction
Scoring
PyRosetta

Hi all,

I am very new to the computational structural biology community and I have tried to model a structure by using a software which runs MODELLER on the background. However, my result shows a number of steric clashes and a very high fa_rep when I calculate it with PyRosetta. I am therefore trying to improve the structure before moving on with the rest of my analysis. 

Post Situation: 

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