Re: Problem with the palmer.py script -- January 08, 2008 - 06:08

Hi again,

I found out that my problem had been proposed as a bug some months ago...

This is bug 8997.

Cheers


Séb


Sebastien Morin wrote:
> Hi all,
>
> I got an error while using the palmer.py script with the 1.2 line of 
> relax (subversion repository).
>
> The data was recorded at only one field for a protein with no 3D structure.
>
> I first tried to run the three stages one after the other (1, 2, 3) with 
> no monte carlo simulations (sims=0). It worked fine and I then wanted to 
> make monte carlo simulations. I put 'sims=500' in the stage 1 and ran 
> it. It worked fine. I then tried to run the stage 2 and got into this 
> error :
>
> =======================
> relax> nuclei(heteronuc='N')
>
> relax> state.load(file='stage1.save', dir=None)
> Opening the file 'stage1.save.bz2' for reading.
>
>
> Loading all the Modelfree 4 data.
>
> relax> palmer.extract(run='m1', dir=None)
> Traceback (most recent call last):
>   File "/home/semor/packages/relax-1.2/relax", line 454, in ?
>     Relax()
>   File "/home/semor/packages/relax-1.2/relax", line 166, in __init__
>     self.interpreter.run()
>   File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 216, 
> in run
>     run_script(intro=self.relax.intro_string, local=self.local, 
> script_file=self.relax.script_file, quit=1)
>   File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 391, 
> in run_script
>     console.interact(intro, local, script_file, quit)
>   File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 343, 
> in interact_script
>     execfile(script_file, local)
>   File "./palmer_2.py", line 129, in ?
>     exec_stage_2(runs)
>   File "./palmer_2.py", line 69, in exec_stage_2
>     palmer.extract(run=name)
>   File "/home/semor/packages/relax-1.2/prompt/palmer.py", line 263, in 
> extract
>     self.__relax__.generic.palmer.extract(run=run, dir=dir)
>   File "/home/semor/packages/relax-1.2/generic_fns/palmer.py", line 578, 
> in extract
>     data.chi2 = float(row[1])
> IndexError: list index out of range
> =======================
>
> Is this a bug or simply am I doing something wrong ?
>
> Thanks !
>
>
> Sébastien
>
>
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>   

--
Sebastien Morin
Etudiant au PhD en biochimie
Laboratoire de resonance magnetique nucleaire
Dr Stephane Gagne
CREFSIP (Universite Laval, Quebec, CANADA)
1-418-656-2131 #4530