Sorry for the delayed response. Work has been quite hectic at the
moment. This is a clear bug, so if you could submit a bug report,
that would be much appreciated. A catch for n == 0 could be added to
fix this problem, but I am very interested in why this situation
occured in the first place. The only reason I can think of right now
is that all 500 Monte Carlo simulations failed! If so, that would be
impressive!
Cheers,
Edward
On Jan 28, 2008 7:01 PM, Sebastien Morin <[EMAIL PROTECTED]> wrote:
>
> Hi,
>
> I recently helped someone use relax and got into a small problem related to
> model elimination, I think.
>
> The script used consisted of minimizing one model-free model, doing Monte
> Carlo simulations, eliminating bad simulations and calculating errors (just
> as in the sample script on page 30, section 6.2.1, of the manual, v1.2.11).
>
> ==================================================================
> #### Script for model-free analysis: model5
> #### Create the run
> name='m5'
> run.create(name,'mf')
> #### Nuclei type
> nuclei('N')
> #### Load the sequence
> sequence.read(name, 'sequence')
> #### Load relaxation data
> relax_data.read(name, 'R1', '600', 599.624 * 1e6, 'AMP-600R1s')
> relax_data.read(name, 'R2', '600', 599.624 * 1e6, 'AMP-600R2s')
> relax_data.read(name, 'NOE', '600', 599.624 * 1e6, 'AMP-600NOEs')
> relax_data.read(name, 'R1', '500', 499.897 * 1e6, 'AMP-500R1s')
> relax_data.read(name, 'R2', '500', 499.897 * 1e6, 'AMP-500R2s')
> relax_data.read(name, 'NOE', '500', 499.897 * 1e6, 'AMP-500NOEs')
> #### Setup other values
> diffusion_tensor.init(name, 6.7 * 1e-9, fixed=1)
> value.set(name, 1.02 * 1e-10, 'bond_length')
> value.set(name, -172 * 1e-6, 'csa')
> #### Select the model-free model
> model_free.select_model(run=name, model=name)
> #### Grid search
> grid_search(name, inc=11)
> #### Minimise
> minimise('newton', run=name)
> #### Monte Carlo simulations
> monte_carlo.setup(name, number=500)
> monte_carlo.create_data(name)
> monte_carlo.initial_values(name)
> minimise('newton', run=name)
> eliminate(run=name)
> monte_carlo.error_analysis(name)
> #### Finish
> results.write(run=name, file=name, force=1)
> ==================================================================
>
> R1s, R2s and NOEs were available from 2 magnetic fields for most residues,
> some of which only had data from 1 magnetic field. For some models
> (5,6,7,8), model elimination eliminated lots of simulations... When reaching
> the 'monte_carlo.error_analysis' call, relax crashed with the following
> error :
>
> ==================================================================
> relax> monte_carlo.error_analysis(run='m5', prune=0.0)
> Traceback (most recent call last):
> File "/usr/local/bin/relax", line 454, in ?
> Relax()
> File "/usr/local/bin/relax", line 166, in __init__
> self.interpreter.run()
> File "/usr/local/packages/relax/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 "/usr/local/packages/relax/prompt/interpreter.py", line 391, in
> run_script
> console.interact(intro, local, script_file, quit)
> File "/usr/local/packages/relax/prompt/interpreter.py", line 343, in
> interact_script
> execfile(script_file, local)
> File "./model5", line 42, in ?
> monte_carlo.error_analysis(name)
> File "/usr/local/packages/relax/prompt/monte_carlo.py", line 145, in
> error_analysis
> self.__relax__.generic.monte_carlo.error_analysis(run=run, prune=prune)
> File "/usr/local/packages/relax/generic_fns/monte_carlo.py", line 220, in
> error_analysis
> Xav = Xsum / float(n)
> ZeroDivisionError: float division
> ==================================================================
>
> It seems 'n' was zero for at least one residue...
>
> Is this something that should be fixed within relax (adding a test that
> would skip error analysis when n=0, but allow the script to end without
> crashing, or adding a more useful error message) ?
>
> Thanks !
>
>
> Séb :)
> --
> 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
>
>
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