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Alternative to MinMover

Submitted by MNP1986 on Tue, 2018-07-31 02:18
Category: 
PyRosetta

Hello everyone,

I have checked the D070_Refinement.py* script provided by the Graylab, and I would like to make my own little refinement script based on it and the other guides and tutorials available.

I have, however, run into problems as the ‘MinMover’ method is not available under pyrosetta.rosetta.protocols.simple_moves which prevents me from using the approach outlined in D070_refinement.py to minimize the pose score.

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PyRosetta - General

installation / python versions

Submitted by rta on Thu, 2018-06-07 00:43
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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PyRosetta - Build/Install

How to use MPI with PyRosetta?

Submitted by sn on Fri, 2018-06-01 15:44
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?

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PyRosetta - Applications

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

Submitted by sn on Thu, 2018-05-24 16:19
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**

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PyRosetta - Build/Install

Folding Video

Submitted by ac.research on Sat, 2018-05-12 09:19
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

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PyRosetta - General

Difference between GenericMonteCarloMover() and GenericSimulatedAnnealer()

Submitted by ac.research on Fri, 2018-05-11 10:37
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:

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PyRosetta - General

PyRosetta Build on Ubuntu 18.04

Submitted by ac.research on Mon, 2018-04-30 22:35
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:

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PyRosetta - Build/Install

PyMOL Update

Submitted by ac.research on Tue, 2018-04-10 22:07
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.

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PyRosetta - General

Coding denovo prediction from density maps in PyRosetta

Submitted by ahmadkhalifa on Tue, 2018-04-10 11:43
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? 

 

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Rosetta 3 - Applications

Multiprocessing and running jobs on server using slurm

Submitted by ahmadkhalifa on Mon, 2018-04-09 10:59
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.

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Rosetta 3 - General

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