Hello everyone,
I am trying to read a silent file with the function poses_from_silent(), but I get an error about an unrecognized residue:
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.
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!
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?
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**
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
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:
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:
I build as per the documented method (which works in older Linux versions):
But I get the following error:
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.
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?
