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pyrosetta source

Category: 
Compilation
PyRosetta

Hi,

I have GLIBC issue with the compiled PyRosetta4.Release.python35.linux.release-191 on a Suse Linux cluster. So I would like to compile it from the source but I cannot find the download link and cannot download it from github using my login details. Kindly suggest the link to download the source code for PyRosetta4.


Regards,


Sarath

Post Situation: 

Introducing N/C-terminal residues to a pose

Category: 
PyRosetta

Hello everyone,

I work with a protein where the crystal structure does not include the first 14 amino acids, which are intrinsically disordered.

I would like to add the missing 14 residues using PyRosetta, and I have therefore looked into the FAQ and tried to find the relevant methods in the documentation.  After some considerations I have come up with strategy:

Post Situation: 

How to make FastRelax use smaller number of rotamers from PyRosetta app?

Category: 
PyRosetta

I am using FastRelax from PyRosetta. When I run it from PyRosetta, the number of rotamers built are way more than the number of rotamers when I run it with C++ relax binary. For instance: I use the following to relax a pdb with movemap in PyRosetta as follows:

def relax_pdb_with_movemap(self, pose, movemap):
        relax = FastRelax()
        relax.set_scorefxn(get_fa_scorefxn())
        relax.set_movemap(movemap)
        relax.apply(pose)
        return pose

In C++ I give the following command:

Post Situation: 

Alternative to MinMover

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.

Post Situation: 

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!

 

Post Situation: 

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: 

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