Re: Error when running full_analysis.y script -- part II -- March 23, 2010 - 15:14

Hi Daniel,

Don't worry about what I said about the diffusion tensor.  I was just
changing some diffusion tensor input code at the time, but the
full_analysis.py doesn't use this anyway. It should be perfectly fine
to use the code as is.

Regards,

Edward



2010/3/17 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> Hi,
>
> The trick here is to have a look at the new full_analysis.py sample
> script.  This has changed quite a lot since relax-1.3.4.  Most of the
> script has been shifted into the core of relax.  Nevertheless you
> should be able to quite easily modify the new script to perform your
> analysis.  There is something that will change soon with the diffusion
> tensor in the 1.3 repository line, so I'll tell you hopefully today
> how to get the change ('svn up' in the relax base directory).
>
> Regards,
>
> Edward
>
>
>
> 2010/3/17 Daniel Pérez <daniel.perez@xxxxxxxxxxxxxxxx>:
> > Hi Edward,
> > thanks for your quick answer.
> > I download the latest of relax 1.3 using
> >
> > $ svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3
> >
> > Now when I run full_analysis.py with it I get the following error message
> >
> > Traceback (most recent call last):
> >   File "/soft/group/relax/relax-1.3/relax", line 358, in ?
> >     Relax()
> >   File "/soft/group/relax/relax-1.3/relax", line 126, in __init__
> >     self.interpreter.run(self.script_file)
> >   File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 287, in 
> > run
> >     return run_script(intro=self.__intro_string, local=locals(),
> > script_file=script_file, quit=self.__quit_flag,
> > show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
> >   File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 533, in
> > run_script
> >     return console.interact(intro, local, script_file, quit,
> > show_script=show_script, raise_relax_error=raise_relax_error)
> >   File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 429, in
> > interact_script
> >     execfile(script_file, local)
> >   File "full_analysis.py", line 674, in ?
> >     Main(self.relax)
> > AttributeError: Interpreter instance has no attribute 'relax'
> >
> >
> > It looks like a pretty basic error, but still I'm stacked with it
> > Regards
> > Daniel
> >
> >
> > Dr. Daniel Pérez
> > Institut für Molekularbiologie und Biophysik
> > Schafmattstrasse 20
> > ETH-Hönggerberg, HPK G 5
> > CH-8093 Zürich
> > Phone: +41 44 633 25 37
> > E-mail: daniel.perez@xxxxxxxxxxxxxxxx
> > Dr. Daniel Pérez
> > Institut für Molekularbiologie und Biophysik
> > Schafmattstrasse 20
> > ETH-Hönggerberg, HPK G 5
> > CH-8093 Zürich
> > Phone: +41 44 633 25 37
> > E-mail: daniel.perez@xxxxxxxxxxxxxxxx
> > On Mar 17, 2010, at 9:58 AM, Edward d'Auvergne wrote:
> >
> > Hi Daniel,
> >
> > This is actually a bug that was fixed a while ago
> > (http://gna.org/bugs/?15050).  I have to release relax-1.3.5 soon as
> > there are many bug fixes in the repository sitting there waiting.  If
> > you can't wait, you can obtain the new code by following the
> > instructions in one of the following:
> >
> > https://mail.gna.org/public/relax-users/2008-09/msg00002.html
> > https://mail.gna.org/public/relax-users/2008-10/msg00013.html
> > https://mail.gna.org/public/relax-users/2006-11/msg00006.html
> >
> > All the links are to help with Google indexing, just like this
> > http://www.nmr-relax.com/ ;)  The first should be enough, but the
> > others might give more info if you need it.
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> > 2010/3/17 Daniel Pérez <daniel.perez@xxxxxxxxxxxxxxxx>:
> >
> > Hi Edward,
> >
> > I hope you have some time to take a look at this. I have a data set at two
> > fields. I used relax for fitting the data, but when and run the
> > full_analysis script, after the software starts the grid search I get the
> > following error message
> >
> > Traceback (most recent call last):
> >
> >  File "/soft/group/relax/relax-1.3.4/relax", line 418, in ?
> >
> >    Relax()
> >
> >  File "/soft/group/relax/relax-1.3.4/relax", line 127, in __init__
> >
> >    self.interpreter.run(self.script_file)
> >
> >  File "/soft/group/relax/relax-1.3.4/prompt/interpreter.py", line 276, in
> > run
> >
> >    return run_script(intro=self.__intro_string, local=self.local,
> > script_file=script_file, quit=self.__quit_flag,
> > show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
> >
> >  File "/soft/group/relax/relax-1.3.4/prompt/interpreter.py", line 537, in
> > run_script
> >
> >    return console.interact(intro, local, script_file, quit,
> > show_script=show_script, raise_relax_error=raise_relax_error)
> >
> >  File "/soft/group/relax/relax-1.3.4/prompt/interpreter.py", line 433, in
> > interact_script
> >
> >    execfile(script_file, local)
> >
> >  File "full_analysis_markup.py", line 764, in ?
> >
> >    Main(self.relax)
> >
> >  File "full_analysis_markup.py", line 226, in __init__
> >
> >    self.multi_model(local_tm=True)
> >
> >  File "full_analysis_markup.py", line 755, in multi_model
> >
> >    grid_search(inc=GRID_INC)
> >
> >  File "/soft/group/relax/relax-1.3.4/prompt/minimisation.py", line 156, in
> > grid_search
> >
> >    minimise.grid_search(lower=lower, upper=upper, inc=inc,
> > constraints=constraints, verbosity=verbosity)
> >
> >  File "/soft/group/relax/relax-1.3.4/generic_fns/minimise.py", line 191, in
> > grid_search
> >
> >    grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
> > verbosity=verbosity)
> >
> >  File
> > "/soft/group/relax/relax-1.3.4/specific_fns/model_free/mf_minimise.py", 
> > line
> > 479, in grid_search
> >
> >    self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
> > constraints=constraints, verbosity=verbosity, sim_index=sim_index)
> >
> >  File
> > "/soft/group/relax/relax-1.3.4/specific_fns/model_free/mf_minimise.py", 
> > line
> > 789, in minimise
> >
> >    model_type = self.determine_model_type()
> >
> >  File "/soft/group/relax/relax-1.3.4/specific_fns/model_free/main.py", line
> > 1015, in determine_model_type
> >
> >    if cdp.diff_tensor.fixed:
> >
> > AttributeError: 'PipeContainer' object has no attribute 'diff_tensor'
> >
> >
> > Checking the mailing archive I saw that Tiago Pais got the same error
> > message last year.
> >
> > That time you suggested him to use a script containing a markup:
> >
> > http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/full_analysis.py?rev=9794&view=markup
> >
> > (
> >
> > The complete answer was:
> >
> > Re: Error when running full_analysis.py script
> >
> > Edward d'Auvergne
> >
> > Tue, 27 Oct 2009 03:02:16 -0700
> >
> > Dear Tiago,
> >
> > This is a hard one to catch.  I have just added a function to this
> >
> > script to check the validity of the user variables
> >
> > (http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/full_analysis.py?rev=9794&view=markup).
> >
> >  This should give better error messages specifically identifying the
> >
> > problem.  For this second issue you are having, it is a little hard to
> >
> > see what the problem is.  Would you be able to supply a little more
> >
> > information.  For example the version of relax you are using, the full
> >
> > error message, how you have executed the full_analysis.py script and
> >
> > at what stage you are up to, etc.  With more information, I should be
> >
> > able to track down the issue.
> >
> > Cheers,
> >
> > Edward
> >
> > )
> >
> >
> >
> > The traceback I showed to you above is coming from running that script, I
> > got the same error message when I run the canonical full_analysis script.
> >
> > I'm running relax 1.3.4 in RHEL distribution 5.1.19.6, kernel /vmlinuz
> > 2.6.18-128.1.10.e15
> >
> > It will be nice if you can help me with this
> >
> > Best regards
> >
> > Daniel
> >
> >
> >
> > Dr. Daniel Pérez
> >
> > Institut für Molekularbiologie und Biophysik
> >
> > Schafmattstrasse 20
> >
> > ETH-Hönggerberg, HPK G 5
> >
> > CH-8093 Zürich
> >
> > Phone: +41 44 633 25 37
> >
> > E-mail: daniel.perez@xxxxxxxxxxxxxxxx
> >
> >
> > _______________________________________________
> >
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> >
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