I used the expression like this:
grid_search(lower=[0.111, 0, 0], upper=[0.111, 2, 1E12], inc=[1, 11, 11])
But I get the following error:
Unconstrained grid search size: 121 (constraints may decrease this size).
Traceback (most recent call last):
File "/usr/local/bin/relax", line 418, in <module>
Relax()
File "/usr/local/bin/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/usr/local/relax/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 "/usr/local/relax/prompt/interpreter.py", line 537, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/usr/local/relax/prompt/interpreter.py", line 433, in
interact_script
execfile(script_file, local)
File "mf_multimodel_m5S2f0111.py", line 82, in <module>
grid_search(lower=[0.111, 0, 0], upper=[0.111, 1, 11], inc=[1, 11, 11])
File "/usr/local/relax/prompt/minimisation.py", line 156, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/usr/local/relax/generic_fns/minimise.py", line 191, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 479,
in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 922,
in minimise
min_options = self.grid_search_config(num_params, spin=spin,
lower=lower, upper=upper, inc=inc, scaling_matrix=scaling_matrix)
File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 554,
in grid_search_config
self.grid_search_config_fin(min_options, lower, upper, scaling_matrix)
File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 631,
in grid_search_config_fin
for i in xrange(n):
NameError: global name 'n' is not defined
Any ideas?
Cheers
Tiago
-----Original Message-----
From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On
Behalf Of Edward d'Auvergne
Sent: quarta-feira, 6 de Abril de 2011 18:05
To: Tiago Pais
Cc: relax-users@xxxxxxx
Subject: Re: How to set S2f to 0.111?
Hi,
These match the parameters as listed in the help for the
model_free.select_model() user function. The grid search arrays match
the parameter arrays.
Regards,
Edward
On 6 April 2011 18:54, Tiago Pais <tpais@xxxxxxxxxxx> wrote:
Ok,
Im sorry to insist but I am probably missing something here. How do I
state
which bound goes with which parameter? That is, which position in the
array
bound corresponds to the S2f parameter?
Regards.
TP
-----Original Message-----
From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On
Behalf Of Edward d'Auvergne
Sent: quarta-feira, 6 de Abril de 2011 17:42
To: Tiago Pais
Cc: relax-users@xxxxxxx
Subject: Re: How to set S2f to 0.111?
Hi,
That is roughly correct. Just set the lower and upper bound to 0.111
and set the number of increments for that parameter to 1. Then it is
like a grid search without S2f being present, or being fixed to 0.111.
Regards,
Edward
On 6 April 2011 18:38, Tiago Pais <tpais@xxxxxxxxxxx> wrote:
Hi Ed,
Thanks for the quick reply.
Let's see if I understand your suggestion. For example, the
mf_multimodel.py
sample script performs a grid search minimization using the grid_search
function. So if I insert an array of upper and lower bounds for the
parameters in the model I can constrain the interval of possible results,
correct? If so, what is the sequence for the parameters in the array?
TP
-----Original Message-----
From: Edward d'Auvergne [mailto:edward.dauvergne@xxxxxxxxx]
Sent: quarta-feira, 6 de Abril de 2011 17:13
To: Tiago Pais
Cc: relax-users@xxxxxxx
Subject: Re: How to set S2f to 0.111?
Hi,
Unfortunately, there is no ability to fix one of the model-free
parameters during optimisation in relax yet. This is something that
has been requested one or two times over the years. This is
complicated as the gradients and Hessians (first and second partial
derivates) need to be modified with this in mind, as the curvature of
the space changes. The fixed parameter is not part of the gradient or
Hessian, and has to be removed. This really complicates the target
function, gradient, and Hessian and, due to the low demand, has not
been implemented.
Are you able to optimise this parameter and see if you get 0.111? And
are you able to extract the timescale of this process (the methyl
group rotamer jumps)? From memory, someone has optimsed these models
using a grid search. This coarse optimisation can be performed in
relax as you are able to specify the fine details of the grid search.
It is slower, but will do the job. You could even implement a zooming
grid search if your scripting skills are up to it to be able to
relatively quickly find the parameters to high precision. Anyway, I
hope this info helps.
Regards,
Edward
On 6 April 2011 17:39, Tiago Pais <tpais@xxxxxxxxxxx> wrote:
Hi,
I would like to make an analysis of side-chain relaxation data with the
S2f
parameter (in model 5) set to 0.111.
Is it possible to do this with RELAX? How?
Thanks in advance.
Cheers
Tiago P
**************************************
Tiago Pais, PhD. student
Cell Physiology & NMR
Instituto de Tecnologia Química e Biológica-Oeiras
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RE: How to set S2f to 0.111?