Hi!
I was not sure if this is 'build/install' question, but it seems that 'general' forum is for more advanced issues..
I'm a beginner in PyRosetta and not really a "tech" person, more wet biologist so sorry if the question is stupid..
Currently using tutorial from http://graylab.jhu.edu/pyrosetta/downloads/documentation/Workshop2_PyRosetta_Intro.pdf to try basics of PyRosetta.
When running pose = pose_from_pdb("1yy8.clean.pdb") got unknown exception error.
Using Ubuntu 16.04.1 LTS 64-bit, python, pyrosetta versions may be seen from log below (is there a way to hide it behind a cut?)
I would be grateful for your advice!
Python 2.7.12 (default, Jul 1 2016, 15:12:24)
Type "copyright", "credits" or "license" for more information.
IPython 2.4.1 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.
In [1]: from pyrosetta import *
In [2]: pyrosetta.init()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-2-34444050a08f> in <module>()
----> 1 pyrosetta.init()
NameError: name 'pyrosetta' is not defined
In [3]: import pyrosetta
In [4]: pyrosetta.init()
Found rosetta database at: /usr/local/lib/python2.7/dist-packages/pyrosetta-4.0-py2.7.egg/database; using it....
PyRosetta-4 2016 [Rosetta 2016 unknown:caf3ac9d7450e125941c5e85236b57d398680305 2016-10-22 12:28:39 -0700] retrieved from: git@github.com:RosettaCommons/main.git
(C) Copyright Rosetta Commons Member Institutions.
Created in JHU by Sergey Lyskov and PyRosetta Team.
core.init: Rosetta version from
core.init: command: PyRosetta -ex1 -ex2aro -database /usr/local/lib/python2.7/dist-packages/pyrosetta-4.0-py2.7.egg/database
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=396660147 seed_offset=0 real_seed=396660147
core.init.random: RandomGenerator:init: Normal mode, seed=396660147 RG_type=mt19937
In [5]: pose = pose_from_pdb("1yy8.clean.pdb")
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-5-c5fc8cfb3b2d> in <module>()
----> 1 pose = pose_from_pdb("1yy8.clean.pdb")
/usr/local/lib/python2.7/dist-packages/pyrosetta-4.0-py2.7.egg/pyrosetta/__init__.pyc in pose_from_pdb(filename)
327 # because otherwise, it wrecks a lot of people's scripts. ~Labonte
328 def pose_from_pdb(filename):
--> 329 return pose_from_file(filename)
330
331
RuntimeError: Caught an unknown exception!
Category:
Post Situation:
sorry, the previous was just because of wrong working directory...
now pose_from_pdb works...
but now I've got an ImportError, can't find toolbox module..
Well, the log file in your post clearly says that PDB file is not there:
Re toolbox module: in PyRosetta-4 it location is changed to pyrosetta.toolbox, please try to import it instead.
Thank's a lot!
You're right, it was my mistake when creating pose.
pyrosetta.toolbox import worked, thank you.
now I've lost PyMOL_mover..
Am I doing smth wrong? I didn't find an answer in pymol_mover tutorial..
Just thought it may be informative, regarding PyMOL_Mover issue,
error happened in the same session, after everything "above" worked (import pyrosetta, pyrosetta.init(), import pyrosetta.toolbox, protein geometry manipulation, pose.dump_pdb. ... PyMOLPyRosettaServer.py worked in PyMOL).
I appreciate your help!
We changed implementation of PyMOL mover from python to C++. So now you need to use something like this:
pymol = pyrosetta.PyMolMover()
It works. Thank you!
Hi,
I have the PyRosetta4.MinSizeRel.python27.linux.release-140 installed on my Windows 8 platform. So far I have been able to pose a pdb structure and am looking forward linking PyMol to Pyrosetta through pymover. I found a post that says that implementation of the pymover is now pymol = pyrosetta.PyMolMover() due to the change from python to C++. However when I enter this command in ipython, I get the AttributeError: "module" object has no attribute "PyMolMover". I will really appreciate any assistance to solve this issue.
Thanks.
Be careful of capitalization: I believe it's pyrosetta.PyMOLMover()