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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: 

Passing a dictionary from pyrosetta to rosetta

Category: 
PyRosetta

Hi,

I'd like to create a function in rosetta (in C++) that ultimately will accept a python dictionary when called from pyrosetta.  What's the best C++ class to use that will be the easiest for me to do the conversion from python dict?  (i.e. is there any existing pyrosetta code that will convert a python dictionary to, say, a C++ map).

Thanks in advance.

Post Situation: 

Import error undefined symbol and Anaconda python

Category: 
PyRosetta

I have a few questions regarding Pyrosetta 4:

First I have Anaconda2 which comes with python installed at /home/MYUSERNAME/anaconda2/bin/python, however the installation uses the default python at /usr/bin/python and its site packages directory in  /usr/lib/python2.7/site-packages.

1) How can I uninstall pyrosetta?

2) How can I install it for the Anaconda python?

 

Second, running native python, trying >>> from rosetta import * gives:

Post Situation: 

Using ref2015 and talaris2014 in the same script

Category: 
PyRosetta

Hi,

I'm using pyrosetta compiled from rosetta_src_2017.39.  I was wondering whether it's possible to use both talaris2014 and ref2015 in the same script.  When I try to set up a scoring function using talaris2014 weights, I get this error:

pyrosetta.create_score_function("talaris2014")

ERROR: talaris2014(.wts) requested, but -corrections::restore_talaris_behavior not set to true. This leads to a garbage scorefunction.  Exiting.

 

Post Situation: 

Using InterfaceSasaFilter

Category: 
PyRosetta

Hi,

I'm trying to use the InterfaceSasaFilter class and am running into an error.  Any idea how to get around this issue?  A snippet of the code is attached, along with the error message

-----------------------

> sasaFilt = pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter()

> sasaFilt.apply(pose)

Post Situation: 

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