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PyRosetta

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.

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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: 

Distorted metal coordination geometry after relaxation (SetupMetalMover was used, fold tree and constraints were set manually)

Category: 
Design
Scoring
Constraints
PyRosetta

 

Hello,

I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.

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Problem Installing PyRosetta/InteractiveROSETTA

Category: 
PyRosetta

I am attempting to install PyRosetta/InteractiveROSETTA on my 64bin Debian Stretch Linux platform and have encountered some problems.

Although the installation of InteractiveRoasetta encountered some problems:
 

Post Situation: 

All self-test.py tests fail after installation

Category: 
PyRosetta

Hello Rosetta community

I am trying to install Pyrosetta3.7 in Linux-windows. The installation appears to go without a hitch. But then when I run the self-test.py script, all tests fail. Error messages look like the one below

Post Situation: 

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