Sorry, forgot to attach the script.
TP
-----Original Message-----
From: Tiago Pais [mailto:tpais@xxxxxxxxxxx]
Sent: terça-feira, 27 de Outubro de 2009 12:17
To: 'Edward d'Auvergne'
Cc: 'Sébastien Morin'; 'Boaz Shapira'; 'relax-users@xxxxxxx'
Subject: RE: Error when running full_analysis.py script
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: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On
Behalf Of Edward d'Auvergne
Sent: terça-feira, 27 de Outubro de 2009 10:02
To: Tiago Pais
Cc: Sébastien Morin; Boaz Shapira; relax-users@xxxxxxx
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 <tpais@xxxxxxxxxxx>:
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:sebastien.morin.1@xxxxxxxxx]
Sent: quarta-feira, 21 de Outubro de 2009 19:46
To: Tiago Pais
Cc: 'Edward d'Auvergne'; 'Boaz Shapira'; relax-users@xxxxxxx
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: relax-users-bounces@xxxxxxx [mailto:relax-users-bounces@xxxxxxx] On
Behalf Of Tiago Pais
Sent: quarta-feira, 21 de Outubro de 2009 15:53
To: 'Edward d'Auvergne'; 'Boaz Shapira'
Cc: relax-users@xxxxxxx
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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--
Sébastien Morin
PhD Student
S. Gagné NMR Laboratory
Université Laval & PROTEO
Québec, Canada
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Re: Error when running full_analysis.py script