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 <[email protected]>:
> 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: [email protected]
> 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: [email protected]
> 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 <[email protected]>:
>
> 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: [email protected]
>
>
> _______________________________________________
>
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>
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