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PyRosetta

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).

 

Post Situation: 

Output several poses in a silent file

Category: 
PyRosetta

Hi,

If I have a list of poses, how can I go about writing a single silent file that contains these poses?  I see there's a SilentFilePoseInputStream class, but I can't find a way to output in silent format.  Can someone point me to those functions?

 

Thanks in advance.

Post Situation: 

PyRosetta compiled with GLIBC 2.12

Category: 
Compilation
PyRosetta

Hello,

We are trying to install PyRosetta on CentOS 6.  The current compilation of PyRosetta (PyRosetta4.Release.python27.linux.release-171.tar.bz2) requires GLIBC_2.14.

However, our system's GLIBC version is 2.12 and the compilation of PyRosetta stop with the error

                          ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cm/shared/apps/pyrosetta/python/2.7/4.171/lib/python2.7/site-packages/pyrosetta-2018.9+release.333d996-py2.7-linux-x86_64.egg/pyrosetta/rosetta.so)

Post Situation: 

Sample dihedral database

Category: 
PyRosetta

Good morning,

 

I have a database of dihedral angles in this order: residue psi psi. Is is possible to use pyrosetta to sample randomly throuh this database,

applying random psi and psi angles to a pdb pose, using a movemap? Imagine that my sequence is AQAAVFGT; so the script would retrieve randomly from the database the dihedrals corresponding to residues in the sequence and output a pose.

is this possible? Maybe with a loop with the SetTorsion mover?

Thank you,

cheers

Post Situation: 

generate_nonstandard_residue_set() takes exactly 2 arguments (1given)

Category: 
PyRosetta

So I'm trying to load this ligand_protein complex PDB into PyRosetta by temporarily creating a ResidueTypeSet

from pyrosetta import *

init()

params_path = Vector1(['cefotaxime.params', 'cefotaxime.params'])

nonstandard_residue_type = generate_nonstandard_residue_set(params_path)

I got this error message:

 

generate_nonstandard_residue_set() takes exactly 2 arguments (1given)

 

Post Situation: 

What is the expected behaviour when minimizing a jump edge?

Category: 
Docking
Constraints
PyRosetta

I have seen references to minimization of a jump edge (e.g using a MinMover object) leading to both rotations and translations downstream of the jump. 

I am modelling an interaction between two proteins, connected in the fold tree by a single jump edge, with atom pair constraints defined to bring them into close proximity.

I allow movement of this jump in the movemap (set_jump), atom_pair_constraints is activated in the scorefunction, and the fold tree is valid.  

Post Situation: 

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