Hi Ed,
I just filed a bug report for this...
Cheers,
Séb
Edward d'Auvergne wrote:
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 <sebastien.morin.1@xxxxxxxxx> 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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--
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
|
Re: Model elimination