Dear Edward,
I will try to provid the most complete information since I have not managed
to solve the problem yet:
1- Relax version 1.3.4 running under Ubuntu 9.04 virtual machine
2- I have executed the script in the command line by typing "relax
full_analysis.py". The location is /home/tpais/ModelFree/PHS/teste/
3- I am in the initial steps of the script with the diffusion model set to
"local_tm".
4-the script still manages to run for a couple of minutes executing some
Newton minimizations and still writes 4 files (tm0, tm1,...) within the
subdirectory "/local_tm". These are the last lines showing up before the
error occurs:
"File "full_analysis.py", line 220, in __init__
self.multi_model(local_tm=True)
File "full_analysis.py", line 662, in multi_model
grid_search(inc=GRID_INC)
File "/usr/local/relax/prompt/minimisation.py", line 156, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/usr/local/relax/generic_fns/minimise.py", line 191, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/usr/local/relax/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 "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 789,
in minimise
model_type = self.determine_model_type()
File "/usr/local/relax/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'"
5- I also send attached the script as I am using it.
By the way, I tried to run the script with the new function and it gave an
indentation error ("IndentationError: expected an indented block") probably
because I copy/past it directly from the link you provided)
Regards,
TiagoP
-----Original Message-----
From: [email protected] [mailto:[email protected]] On
Behalf Of Edward d'Auvergne
Sent: terça-feira, 27 de Outubro de 2009 10:02
To: Tiago Pais
Cc: Sébastien Morin; Boaz Shapira; [email protected]
Subject: Re: Error when running full_analysis.py script
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=97
94&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
2009/10/22 Tiago Pais <[email protected]>:
> Hi Sebastien,
> The thing is it was not exactly an error of the script. In the line 639
you
> have to adjust the script so that it agrees with the format of the
function
> that you have used in line 174 "Relax_Data=[...". If in line 174 you
> describe the data sets with only three parameters (e.g.[Rilabel, freq,
> file]) then, in line 639 you have to adapt the function so that the
program
> reads only three sets of parameters (e.g. relax_data.read(data[0],
data[1],
> data[2], data[3]) while in the original file was set to read 13.
> This is beginners' stuff, but that's exactly what I am with respect to
RELAX
> and PYTHON, so it may be usefull for other beginners.
>
> However, I still have not managed to run the script to the end. At the
> moment I am stuck with yet another error message: AttributeError:
> 'PipeContainer' object has no attribute 'diff_tensor'
>
> If anyone can help me and avoid that I loose time with this probably easy
to
> solve error, please do.
> Thanks
> Tiago P
>
> -----Original Message-----
> From: Sébastien Morin [mailto:[email protected]]
> Sent: quarta-feira, 21 de Outubro de 2009 19:46
> To: Tiago Pais
> Cc: 'Edward d'Auvergne'; 'Boaz Shapira'; [email protected]
> Subject: Re: Error when running full_analysis.py script
>
> Dear Tiago,
>
> Just for the logs, could you tell us what was the problem ?
>
> Regards,
>
>
> Sébastien
>
>
> Tiago Pais wrote:
>> Ok, managed to solve this already.
>> Cheers
>> Tiago
>>
>> -----Original Message-----
>> From: [email protected] [mailto:[email protected]] On
>> Behalf Of Tiago Pais
>> Sent: quarta-feira, 21 de Outubro de 2009 15:53
>> To: 'Edward d'Auvergne'; 'Boaz Shapira'
>> Cc: [email protected]
>> Subject: Error when running full_analysis.py script
>>
>> Dear all,
>> I am using 15N relaxation data previously analyzed to test some of the
>> scripts available in Relax to make sure that I am using it correctly.
>> However, I get the following error message when running the sample script
>> full_analysis.py: "List Index out of Range"
>> Below is "print screen" where the error shows up at the bottom:
>>
>> "None 149 Q None None
>>
>> relax> spin.name(spin_id=None, name='N', force=False)
>> Traceback (most recent call last):
>> File "/usr/local/bin/relax", line 418, in <module>
>> Relax()
>> File "/usr/local/bin/relax", line 127, in __init__
>> self.interpreter.run(self.script_file)
>> File "/usr/local/relax/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 "/usr/local/relax/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 "/usr/local/relax/prompt/interpreter.py", line 433, in
>> interact_script
>> execfile(script_file, local)
>> File "full_analysis.py", line 671, in <module>
>> Main(self.relax)
>> File "full_analysis.py", line 220, in __init__
>> self.multi_model(local_tm=True)
>> File "full_analysis.py", line 639, in multi_model
>> relax_data.read(data[0], data[1], data[2], data[3], data[4], data[5],
>> data[6], data[7], data[8], data[9], data[10], data[11],
>> data[12])
>> IndexError: list index out of range"
>>
>> I can't understand if the error relates to the last command listed,
> actually
>> I can't understand the command given in this line (639) - what is it
> suppose
>> to do?
>>
>> Best regards
>> TiagoP
>>
>>
>> _______________________________________________
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>>
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>>
>> _______________________________________________
>> relax (http://nmr-relax.com)
>>
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>
>
> --
> Sébastien Morin
> PhD Student
> S. Gagné NMR Laboratory
> Université Laval & PROTEO
> Québec, Canada
>
>
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