Member Site › Forums › PyRosetta › PyRosetta – Applications › Problem with PyRosetta install
- This topic has 2 replies, 2 voices, and was last updated 10 years, 3 months ago by
Anonymous.
-
AuthorPosts
-
-
May 21, 2014 at 4:11 pm #1893
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.posePROBLEM 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.poseQUESTION 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/rosettabut none of these directories contains: core protocols etc
— these directories are in $ROSETTA/main/source/src/python/bindings/src
-
May 23, 2014 at 8:59 pm #10066
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.
-
May 27, 2014 at 9:48 pm #10070
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 directoryI actually have two pythons libs installed:
/usr/lib64/libpython2.7.so
/usr/lib64/libpython3.soIf 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.
-
-
AuthorPosts
- You must be logged in to reply to this topic.