Re: [bug #13259] full analysis-high Te values -- September 14, 2009

Hi Ed,

Yes, the grid search might be a bit long...

The error
    "AttributeError: 'PipeContainer' object has no attribute 'chi2'"
is no problem.

The important thing is to look in the results file (in the aic
sub-directory) and see that the 'ts' value for ALA44 is ~ 20ns...

Regards,


Séb




Edward d'Auvergne wrote:

Seb,

I've downloaded and unpacked the tar file.  I then ran:

$ relax full_analysis_modified.py

This started a calculation (the grid search took far too long for a
system test), and the last print outs were:


-----
Parameter values: array([  9.00134731e+03,   6.44630021e-16,  
-2.80379884e-01,
        -6.87605719e-01,   9.47607578e-01,   6.45728529e+01,
         9.47607578e-01,   1.70166648e+04,   4.48411813e-18])
Function value:   17.649643455012111
Iterations:       58
Function calls:   716
Gradient calls:   65
Hessian calls:    58
Warning:          None


relax> results.write(file='results', dir='prolate/round_2/opt',
force=True, compress_type=1)
Opening the file 'prolate/round_2/opt/results.bz2' for writing.




#####################
# Convergence tests #
#####################


Chi-squared test:
Traceback (most recent call last):
  File "/data/relax/relax-1.3/relax", line 420, in <module>
    Relax()
  File "/data/relax/relax-1.3/relax", line 128, in __init__
    self.interpreter.run(self.script_file)
  File "/data/relax/relax-1.3/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 "/data/relax/relax-1.3/prompt/interpreter.py", line 545, in 
run_script
    return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
  File "/data/relax/relax-1.3/prompt/interpreter.py", line 441, in
interact_script
    exec(compile(open(script_file).read(), script_file, 'exec'), local)
  File "full_analysis_modified.py", line 677, in <module>
    Main(self.relax)
  File "full_analysis_modified.py", line 317, in __init__
    converged = self.convergence()
  File "full_analysis_modified.py", line 416, in convergence
    print(("    chi2 (k-1):          " + repr(prev_pipe.chi2)))
AttributeError: 'PipeContainer' object has no attribute 'chi2'
-----


Is this what is supposed to happen?

Cheers,

Edward


2009/9/4 Sébastien Morin <NO-REPLY.INVALID-ADDRESS@xxxxxxx>:

Follow-up Comment #11, bug #13259 (project relax):

Hi,

Here is a minimal dataset that reproduces the problem.

The script enclosed ('full_analysis_modified.py') will make minimisation
round 'round_2', minimising models 'm1' and 'm8' and proceeding to aic 
model
selection. There, model 'm8' will be chosen for residue ALA44 despite a ts 
of
~2e-8 (20 ns).

The failure of the script after the aic step is normal and of no importance
for this bug (it is just a result of the hacking of the script)...


Séb

(file #6572)
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-- 
Sébastien Morin
PhD Student
S. Gagné NMR Laboratory
Université Laval & PROTEO
Québec, Canada

Re: [bug #13259] full analysis-high Te values

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