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installation / python versions

Category: 
PyRosetta

Hi,

I would like to install PyRosetta4 for python 3.6 on Ubuntu 16.04 64bit. For this I installed python3.6, as deafault python version was 2.7. According the installation instruction I have to use smth like

cd setup && sudo python setup.py install

Will it call python 2.7? should I expect any errors? How should I install PyRosetta properly?

Thanks!

 

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How to use MPI with PyRosetta?

Category: 
PyRosetta

Hi,

I am trying to parallelize a protocol using MPI in PyRosetta. I see that PyRosetta does provide interfaces for MPI based job distributors. But, I also saw a documentation stating that PyRosetta doesn't support MPI (https://www.rosettacommons.org/docs/latest/build_documentation/TACC) and recommends using MPI framework provided by Python using mpi4py library. 

Is MPI supported within PyRosetta? How does one typically parallelize PyRosetta protocols?

Post Situation: 

Dunbrack library takes a very long time to load with custom build

Category: 
PyRosetta

Hi,

I built PyRosetta from scratch with the latest release of Rosetta (2018.19).

Below are the cofigurations of my system:

OS details: CentOS Linux 6.7 64 bit cluster 

Python version 3.6 64 bit

I was successfully able to build the PyRosetta source. However, when I try to run a custom protocol, the Dunbrack library takes a very long time to load. Below is the output after the library loads:

**Dunbrack 2010 library took 618.78 seconds to load from ASCII**

Post Situation: 

Folding Video

Category: 
PyRosetta

Dear Everyone,

 

I think I heard somewhere that it is possible to capture a video of an abinitio fold from pyrosetta on PyMOL? can someone point me to where I can learn how to do that? I would like to show a folding video of my protein in a presentation.

 

Thanks

Post Situation: 

Difference between GenericMonteCarloMover() and GenericSimulatedAnnealer()

Category: 
PyRosetta

Hello Everyone,

I am trying to preform RosettaDesign using thr FastRelax() mover. As I understand this is the correct mover? or should i be using FastDesign()?

Anyway, What is the difference between the GenericMonteCarloMover() and the GenericSimulatedAnnealer() movers? and which one should I be using with FastRelax() to preform correct RosettaDesign?

I tried both, but both fail to change the structure's sequence. Here is my code:

Post Situation: 

PyRosetta Build on Ubuntu 18.04

Category: 
PyRosetta

Hello everyone,

I want to draw your attention that I am failing to build PyRosetta on the new Ubuntu 18.04 (released last week).

My setup:

  • Ubuntu Linux 18.04 64bit (server)
  • Python 3.6.5
  • PyRosetta 4 python36 ubuntu release 177

 

I build as per the documented method (which works in older Linux versions):

  • tar -vjxf {PYROSETTA}.tar.bz2
  • sudo python3 {PYROSETTA}/setup/setup.py install

But I get the following error:

Post Situation: 

PyMOL Update

Category: 
PyRosetta

Dear Developers,

 

PyMOL has just been updated to use Python 3 by default, thus the PyMOL-RosettaServer.py script to view the structure changes in PyMOL no longer works.

The print statements needs to be changed as well as the 'from cStringIO import StringIO' along with other changes to update the script from python 2 to python 3.

 

I hope this helps.

Post Situation: 

Coding denovo prediction from density maps in PyRosetta

Category: 
PyRosetta

I want to code the below scripts using PyRosetta. I'm totally new to Pyrosetta, only starting to read the tutorials today. However, I know Python very well. Anyway, all the scripts seem to be calling the denovo_density.linuxgccrelease binary so I'm guessing, if there's a Pyrosetta class or module built on that, it shouldn't be but a few lines of code.

My qustions are, can it be done? How? 

 

Post Situation: 

Multiprocessing and running jobs on server using slurm

Category: 
Structure prediction
PyRosetta

I have a question regarding parallelizing some of the bash scripts from the refinement and denovo prediction tutorials. They usually rely on GNU parallel to run across many cores, substituting some variable in the script with a number from the GNU parallel run command . I wonder how I can run the same scripts on a server running slurm workload manager, or any other possible multiprocessing strategy using Python.

Post Situation: 

cleanATOM() for non-ideal amino acids

Category: 
PyRosetta

Hello People,

 

I am trying to clean this protein 3HZ7.pdb using pyrosetta.toolbox.cleaning.cleanATOM('3HZ7.pdb') in order to use it within PyRosetta.

The protein has MSE (Selenomethionine?) instead of MET at different parts of the sequence, therefore when applying cleanATOM() it just deletes these amino acids and I end up with a broken backbone (attached figure).

 

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