Re: [modeller_usage] mutate script from modeller site
To: DimitryASuplatov <>
Subject: Re: [modeller_usage] mutate script from modeller site
From: Modeller Caretaker <>
Date: Tue, 11 Nov 2008 08:43:21 -0800
> I am trying to use mutate.py script from modeller site
> I have python2.5 core and devel packages installed. When I run
>> mod9v5 - 1klc.nodummies.chains.pdb 500 ARG B < mutate.py > out
> (according to the instructions in the header of the script)
> I get the following error
> 'import site' failed; use -v for traceback
> Traceback (most recent call last):
> File "(stdin)", line 2, in ?
> ImportError: No module named os
See #2 at http://salilab.org/modeller/release.html#issues
Modeller has a built-in copy of the Python 2.3 interpreter, but you
don't have the 2.3 modules installed (you have 2.5). As you go on to
discover, you can't mix and match 2.5 modules with the 2.3 interpreter.
The solution detailed in the release notes is not to use 'mod9v5' to run
your script, but instead to treat it as a 'normal' Python script and use
your system's "python" binary to run it. In order for this to work
though, the Modeller Python libraries need to be in your Python path,
and this depends on how you installed Modeller.
If you installed from the RPM, everything should be already set up for
you. Just replace your command line with
python mutate.py 1klc.nodummies.chains.pdb 500 ARG B > out
If you installed from the .tar.gz, the installer will have told you how
to set up the paths so that the above command line works. Alternatively,
you can prefix that command line with
(where <TOP> is the directory you installed Modeller in) to set the
paths just for that script.
Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage