Problem with PyRosetta install

[Anonymous]

Dear Rosetta gurus,

I thought I was pretty fluent in python, yet, I stumble on serious problems while trying to use D020_Pose_scoring.py — essentially a rosetta package is missing.
thus, I had two questions:

1. do I miss a key install recommendation?
2. since I am interested in scoring, is there a tutorial on the C++ functionalities offered for scoring?

thanks a lot and best regards, Frederic Cazals.

— we installed rosetta and set the following env. variables:

setenv ROSETTA ${HOME}/PACKAGES/INSTALL/x86_64/rosetta/rosetta_2014.18.56749_bundle
setenv PYTHONPATH ${ROSETTA}/tools/protein_tools/rosettautil:${ROSETTA}/main/source/src/python/bindings/src

— we tried to play with the demos in
$ROSETTA/main/source/src/python/bindings/demos, but faced various errors:

cabestan-fcazals> python D020_Pose_scoring.py
Traceback (most recent call last):
File “D020_Pose_scoring.py”, line 67, in
from PyMolLink import *
File “/user/fcazals/home/PACKAGES/INSTALL/x86_64/rosetta/rosetta_2014.18.56749_bundle/main/source/src/python/bindings/src/PyMolLink.py”, line 29, in
import rosetta.core.pose
ImportError: No module named core.pose

PROBLEM 1:

$ROSETTA/main/source/src/python/bindings/src/PyMolLink.py contains
56:from rosetta.PyMolLink import *

QUESTION: where is the package rosetta?

PROBLEM 2:

if we change the previous import by removing the rosetta. that is

from PyMolLink import *

and since PYTHONPATH contains the source directory containing
PyMolLink.py, we expect good news. unfortunately:

cabestan-fcazals> python D020_Pose_scoring.py
Traceback (most recent call last):
File “D020_Pose_scoring.py”, line 67, in
from PyMolLink import *
File “/user/fcazals/home/PACKAGES/INSTALL/x86_64/rosetta/rosetta_2014.18.56749_bundle/main/source/src/python/bindings/src/PyMolLink.py”, line 29, in
import rosetta.core.pose
ImportError: No module named core.pose

QUESTION AGAIN: we do not find the rosetta package with
core/protocols/etc as sub-directories?

Indeed:

cabestan-fcazals> cd $ROSETTA
cabestan-fcazals> find . -name rosetta
./main/source/src/python/apps/public/protein_tools/rosettautil/rosetta
./tools/protein_tools/rosettautil/rosetta

but none of these directories contains: core protocols etc

— these directories are in $ROSETTA/main/source/src/python/bindings/src

[Anonymous]

Hi Frederic,

From your comment it looks like you downloaded the academic release version of Rosetta. Is this correct? If so, then this is *source-code-package* and it does not contain PyRosetta binaries. So to use PyRosetta you will need ether download one of PyRosetta builds from http://www.pyrosetta.org or build it. I would recommend starting with trying binaries first.

[Anonymous]

Dear Sergey,

thanks for the tip. one more (and hopefully last) question: we installed PyRosetta.ScientificLinux-r56324.64Bit.tar.bz2

but upon launching python D020_Pose_scoring.py, we get:
ImportError: libpython2.6.so.1.0: cannot open shared object file: No such file or directory

I actually have two pythons libs installed:
/usr/lib64/libpython2.7.so
/usr/lib64/libpython3.so

If I visit python.org, from https://www.python.org/download/releases/2.6, one reads:

Python 2.6 has been replaced by a newer bugfix release of Python. Please download Python 2.6.7 instead. This is a source-only release.

question: is there a way to couple PyRosetta.ScientificLinux-r56324.64Bit.tar.bz2 to a more recent version of python?

thanks again for your help, Frederic.

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