error while installing pyrosetta – lack of a module named “rosetta”

[Anonymous]

Hello,

I’ve got a problem with installing pyrosetta. I have already built it.
When trying to install it, the following error occurs :

Traceback (most recent call last):
File “pyrosetta_toolkit.py”, line 16, in
from rosetta import *
ImportError: No module named rosetta

What should I do? Where can I find that module named “rosetta”?

Thank you in advance

PS I use Linux Ubuntu 12.4 and python 2.7.3

[Anonymous]

Hi Mimi,

Can you be more specific? Did you build it from c++ source code? What do you mean install it?

Are you trying to use the GUI pyrosetta_toolkit, or use PyRosetta for scripting?

The error that you’re getting is from not setting up the paths to PyRosetta. Please see http://www.pyrosetta.org/dow and http://graylab.jhu.edu/pyrosetta/downloads/documentation/pyrosetta_toolkit/pyrosetta_toolkit.html if you are trying to use the GUI.

Check to make sure you can import the Rosetta module after you have setup the paths by typing ‘from rosetta import *’ in a python shell.

-Jared

[Anonymous]

Hi, Jared

> Did you build it from c++ source code?

Well, I think so….

> Are you trying to use the GUI pyrosetta_toolkit, or use PyRosetta for scripting?

Actually, both of them.

How can I set the paths to module Rosetta? I couldn’t find any module with such name (well, I found an empty folder named “Rosetta” in rosetta_source/bin)…

Thanks for your response!

[Anonymous]

Hi Mimi, I would recommend downloading the precompiled binaries from http://www.PyRosetta.org they are extremely current, and might be easier to set up.

They are much more current than 3.4 Rosetta, though 3.5 comes close.

Can you say how you built it? Did you use the extras=PyRosetta when building Rosetta? Are you a developer and using trunk Rosetta?

If the build was successful, the path to the binaries is Rosetta_source/src/python/bindings. Look at setPyrosettaEnvironment.sh.
You may need to change the default path for Rosetta_database in that file as it’s not usually compiled from released C++ source.

You should also look at the tips section of the GUI documentation. This shows you how to setup your bashrc file so you wouldn’t need to run setPyrosettaEnvironment every time you want to import Rosetta into python, or each time you would want to use the gui.

Let us know how it goes.

-J

[Anonymous]

Mimi, if your build was successful then you should see Rosetta_source/src/python/bindings/rosetta dir. Could you please check if it there?

[Anonymous]

Hi,

I’m extremely sorry for not responding earlier, but I was travelling.

> Mimi, if your build was successful then you should see Rosetta_source/src/python/bindings/rosetta dir. Could you please check if it there?

I checked this directory and it’s not there…

jadolfbr – I’m going to build rosetta once again and consider all your pieces of advice. I’ll let you know how it goes!

Thanks a lot!

[Anonymous]

Hi,

Problem with that module rosetta disappeared(thanks) but I came across another erros, when trying to run pyrosetta_toolkit.py :

” Traceback (most recent call last):
File “./pyrosetta_toolkit.py”, line 16, in
from rosetta import *
File “/home/lisa/PyRosetta.Ubuntu-12.04LTS-r55460.64Bit/rosetta/__init__.py”, line 30, in
import utility
File “/home/lisa/PyRosetta.Ubuntu-12.04LTS-r55460.64Bit/rosetta/utility/__init__.py”, line 1, in
from __utility_all_at_once_ import *
ImportError: /home/lisa/PyRosetta.Ubuntu-12.04LTS-r55460.64Bit/rosetta/utility/__utility_all_at_once_.so: wrong ELF class: ELFCLASS64

I’m sorry to bother you again, but I feel lost….

-Mimi

[Anonymous]

Hi Mimi,

This means that you are running the 64bit version of PyRosetta on a 32 bit system architecture (or sometimes a 32 version of the OS). Search wrong ELF class on the forums, and you will find some suggestions. However, 32 bit ubuntu version are not compiled any more for distributed binaries, so you may have to upgrade your computer or find a different computer to use PyRosetta on it if it is a 32 bit system. You could also try an older version of PyRosetta (2.0 beta ubuntu). This version will not have the GUI, and will have some missing Rosetta functionality, possibly more bugs – but for basic scripting it should work.

-Jared

[Anonymous]

Thank you very much!
Actually I have a 64-bit architecture, but I’m using 32-version of the OS… so now everything is clear… Thanks a lot!

[Author]

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