Re: error messages with model=final and Monte carlo output -- October 20, 2006

On Fri, 2006-10-20 at 13:19 +0200, Daniel Perez wrote:

Hi Ed,

I ran calculations using full_analysis.py with two data sets. After 
runing the diffusion models and getting convergence for all of them I 
tryed with the model=final. I got the following error messages:

Dataset 1, model=final

Traceback (most recent call last):
   File "/home/perez/relax-1.2.6/relax", line 419, in ?
     Relax()
   File "/home/perez/relax-1.2.6/relax", line 151, in __init__
     self.interpreter.run()
   File "/home/perez/relax-1.2.6/prompt/interpreter.py", line 213, in run
     run_script(intro=self.relax.intro_string, local=self.local, 
script_file=self.relax.script_file, quit=1)
   File "/home/perez/relax-1.2.6/prompt/interpreter.py", line 385, in 
run_script
     console.interact(intro, local, script_file, quit)
   File "/home/perez/relax-1.2.6/prompt/interpreter.py", line 340, in 
interact_script
     execfile(script_file, local)
   File "final.py", line 419, in ?
     Main()
   File "final.py", line 263, in __init__
     self.model_selection(run='final', write_flag=0)
   File "final.py", line 349, in model_selection
     eliminate()
   File "/home/perez/relax-1.2.6/prompt/eliminate.py", line 97, in eliminate
     self.relax.generic.eliminate.eliminate(run=run, function=function, 
args=args)
   File "/home/perez/relax-1.2.6/generic_fns/eliminate.py", line 69, in 
eliminate
     names = param_names(self.run, i)
   File "/home/perez/relax-1.2.6/specific_fns/model_free.py", line 1448, 
in get_param_names
     if not self.relax.data.res[self.run][j].model:
AttributeError: Element instance has no attribute 'model'


Dataset 2, model=final

Traceback (most recent call last):
   File "/home/perez/relax-1.2.6/relax", line 419, in ?
     Relax()
   File "/home/perez/relax-1.2.6/relax", line 151, in __init__
     self.interpreter.run()
   File "/home/perez/relax-1.2.6/prompt/interpreter.py", line 213, in run
     run_script(intro=self.relax.intro_string, local=self.local, 
script_file=self.relax.script_file, quit=1)
   File "/home/perez/relax-1.2.6/prompt/interpreter.py", line 385, in 
run_script
     console.interact(intro, local, script_file, quit)
   File "/home/perez/relax-1.2.6/prompt/interpreter.py", line 340, in 
interact_script
     execfile(script_file, local)
   File "final.py", line 418, in ?
     Main()
   File "final.py", line 274, in __init__
     monte_carlo.create_data('final')
   File "/home/perez/relax-1.2.6/prompt/monte_carlo.py", line 91, in 
create_data
     self.__relax__.generic.monte_carlo.create_data(run=run, method=method)
   File "/home/perez/relax-1.2.6/generic_fns/monte_carlo.py", line 78, 
in create_data
     data = create_mc_data(self.run, i)
   File "/home/perez/relax-1.2.6/specific_fns/model_free.py", line 639, 
in create_mc_data
     value = self.back_calc(run=run, index=i, 
ri_label=self.relax.data.res[run][i].ri_labels[j], 
frq_label=self.relax.data.res[run][i].frq_labels[self.relax.data.res[run][i].remap_table[j]],
 
frq=self.relax.data.res[run][i].frq[self.relax.data.res[run][i].remap_table[j]])
   File "/home/perez/relax-1.2.6/specific_fns/model_free.py", line 398, 
in back_calc
     value = self.minimise(run=self.run, min_algor='back_calc', 
min_options=(index, ri_label, frq_label, frq))
   File "/home/perez/relax-1.2.6/specific_fns/model_free.py", line 2024, 
in minimise
     if not self.relax.data.res[self.run][i].model:
AttributeError: Element instance has no attribute 'model'


Yeah, I gave up with windows... I have only one computer with windows 
and it was toooooo slow. With the Linux network it is a piece of cake to 
spread the jobs, and with parallel calculation it make sense.

About the error messages they may be related with the fact that the 
local-tm was the model with the lowest chi square, I do not know.


I've seen this before, and you are right. It simply reflects the fact
that the local-tm model has been selected as the best treatment of
overall diffusion. Monte-Carlo simulations are failing because the data
structures are slightly different in this case. Would you mind
submitting a bug report for this:
https://gna.org/bugs/?group=relax

Thanks,

Chris

PS. it is worth looking carefuly at why local-tm is the best diffusion
model. It might suggest that your protein's dynamics are a bit unusual,
or it might reflect a problem in the data somewhere.


Well, knowing that this protein does not fit any diffusion tensor I used 
relax to sample the reduced spectral density function. I obtained the 
list containing the fitted values for J(0), J(N), J(H), and the 
corresponding errors. But, in addition you provide with a list of ALL 
the Montecarlo simulations. What do you suggest to do with it?

Best Regards

Daniel

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Re: error messages with model=final and Monte carlo output

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