Re: relaxation curve fitting
Hi Romel,
I hope you don't mind, but I have taken your test data and script and
created a relax system test with it. I have only included the data
for residues 24, 28, and 29, and have not used the PDB file. The data
will be located in the directory
test_suite/shared_data/peak_lists/bug_19887, and the script is called
test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py.
If you'd like to keep it secret, I can randomise the peak heights a
little if you like. I can now reproduce the problem by running this
specific test with:
$ relax -s Relax_fit.test_bug_19887_curvefit_fail
To perform this test yourself, you'd need the subversion program
installed. If you have this, you can get the most up-to-date copy of
relax (and the minfx and bmrblib libraries) by typing:
$ svn co http://svn.gna.org/svn/relax/trunk relax-trunk
$ cd relax-trunk
$ svn co http://svn.gna.org/svn/minfx/trunk/minfx
$ svn co http://svn.gna.org/svn/bmrblib/trunk/bmrblib
This might be needed later to obtain the fixes.
Regards,
Edward
On 2 July 2012 10:38, Edward d'Auvergne wrote:
> Cheers! Hopefully I'll be able to reproduce the problem and come up
> with a fix soon.
>
> Regards,
>
> Edward
>
>
>
> On 2 July 2012 10:32, Romel Bobby wrote:
>> Hi Edward,
>>
>> I've submitted the bug under #19887 and included the output of 'relax
>> --info' in relax_info.txt. I also included tar.gz file containing all the
>> input files (ie lists for relaxation delays, pdb, log file, etc.).
>> Thanks
>>
>> Kind regards,
>>
>> Romel
>>
>>
>> On 2 July 2012 19:29, Edward d'Auvergne wrote:
>>>
>>> Hi,
>>>
>>> This appears to be a unique bug! I would guess that it has something
>>> to do with the software versions in use - on most systems this code
>>> path works flawlessly. But I should be able to modify relax to handle
>>> this. Would you be able to please make a bug report? The link is
>>> https://gna.org/bugs/?func=additem&group=relax. If you could include
>>> a short description, the error message, and the output of 'relax
>>> --info', this would be of significant help. If possible, I would like
>>> to try to catch this in the relax test suite. The more information
>>> you provide the better - because if I can reproduce the problem on my
>>> computer, I can then fix the problem within minutes. Otherwise it
>>> takes much, much longer.
>>>
>>> Cheers,
>>>
>>> Edward
>>>
>>>
>>>
>>> On 30 June 2012 21:16, Romel Bobby wrote:
>>> > Hi Edward,
>>> >
>>> > I tried the 'exp' model and it gave me the very same error message (see
>>> > below).
>>> >
>>> > File "/usr/local/relax/multi/processor.py", line 480, in run
>>> > self.callback.init_master(self)
>>> > File "/usr/local/relax/multi/__init__.py", line 319, in
>>> > default_init_master
>>> > self.master.run()
>>> > File "/usr/local/relax/relax.py", line 183, in run
>>> > self.interpreter.run(self.script_file)
>>> > File "/usr/local/relax/prompt/interpreter.py", line 280, in run
>>> > return run_script(intro=self.__intro_string, local=locals(),
>>> > 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 570, 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 455, in
>>> > interact_script
>>> > exec_script(script_file, local)
>>> > File "/usr/local/relax/prompt/interpreter.py", line 329, in
>>> > exec_script
>>> > runpy.run_module(module, globals)
>>> > File
>>> >
>>> > "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
>>> > line 180, in run_module
>>> > fname, loader, pkg_name)
>>> > File
>>> >
>>> > "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
>>> > line 72, in _run_code
>>> > exec code in run_globals
>>> > File "/Users/b_romel/temp_relax/backup/relax_fit.py", line 87, in
>>> >
>>> > grid_search(inc=11)
>>> > File "/usr/local/relax/prompt/uf_objects.py", line 220, in __call__
>>> > self._backend(*new_args, **uf_kargs)
>>> > File "/usr/local/relax/generic_fns/minimise.py", line 141, in
>>> > grid_search
>>> > grid_search(lower=lower, upper=upper, inc=inc,
>>> > constraints=constraints,
>>> > verbosity=verbosity)
>>> > File "/usr/local/relax/specific_fns/relax_fit.py", line 609, 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/relax_fit.py", line 716, in
>>> > minimise
>>> > if constraints and not match('^[Gg]rid', min_algor):
>>> > File
>>> > "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/re.py",
>>> > line 137, in match
>>> > return _compile(pattern, flags).match(str
Re: relaxation curve fitting
Cheers! Hopefully I'll be able to reproduce the problem and come up
with a fix soon.
Regards,
Edward
On 2 July 2012 10:32, Romel Bobby wrote:
> Hi Edward,
>
> I've submitted the bug under #19887 and included the output of 'relax
> --info' in relax_info.txt. I also included tar.gz file containing all the
> input files (ie lists for relaxation delays, pdb, log file, etc.).
> Thanks
>
> Kind regards,
>
> Romel
>
>
> On 2 July 2012 19:29, Edward d'Auvergne wrote:
>>
>> Hi,
>>
>> This appears to be a unique bug! I would guess that it has something
>> to do with the software versions in use - on most systems this code
>> path works flawlessly. But I should be able to modify relax to handle
>> this. Would you be able to please make a bug report? The link is
>> https://gna.org/bugs/?func=additem&group=relax. If you could include
>> a short description, the error message, and the output of 'relax
>> --info', this would be of significant help. If possible, I would like
>> to try to catch this in the relax test suite. The more information
>> you provide the better - because if I can reproduce the problem on my
>> computer, I can then fix the problem within minutes. Otherwise it
>> takes much, much longer.
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>> On 30 June 2012 21:16, Romel Bobby wrote:
>> > Hi Edward,
>> >
>> > I tried the 'exp' model and it gave me the very same error message (see
>> > below).
>> >
>> > File "/usr/local/relax/multi/processor.py", line 480, in run
>> > self.callback.init_master(self)
>> > File "/usr/local/relax/multi/__init__.py", line 319, in
>> > default_init_master
>> > self.master.run()
>> > File "/usr/local/relax/relax.py", line 183, in run
>> > self.interpreter.run(self.script_file)
>> > File "/usr/local/relax/prompt/interpreter.py", line 280, in run
>> > return run_script(intro=self.__intro_string, local=locals(),
>> > 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 570, 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 455, in
>> > interact_script
>> > exec_script(script_file, local)
>> > File "/usr/local/relax/prompt/interpreter.py", line 329, in
>> > exec_script
>> > runpy.run_module(module, globals)
>> > File
>> >
>> > "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
>> > line 180, in run_module
>> > fname, loader, pkg_name)
>> > File
>> >
>> > "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
>> > line 72, in _run_code
>> > exec code in run_globals
>> > File "/Users/b_romel/temp_relax/backup/relax_fit.py", line 87, in
>> >
>> > grid_search(inc=11)
>> > File "/usr/local/relax/prompt/uf_objects.py", line 220, in __call__
>> > self._backend(*new_args, **uf_kargs)
>> > File "/usr/local/relax/generic_fns/minimise.py", line 141, in
>> > grid_search
>> > grid_search(lower=lower, upper=upper, inc=inc,
>> > constraints=constraints,
>> > verbosity=verbosity)
>> > File "/usr/local/relax/specific_fns/relax_fit.py", line 609, 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/relax_fit.py", line 716, in
>> > minimise
>> > if constraints and not match('^[Gg]rid', min_algor):
>> > File
>> > "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/re.py",
>> > line 137, in match
>> > return _compile(pattern, flags).match(string)
>> > TypeError: bad argument type for built-in operation
>> >
>> > Regards,
>> >
>> > Romel
>> >
>> > On 1 July 2012 06:42, Edward d'Auvergne wrote:
>> >>
>> >> Hi Romel,
>> >>
>> >> The problem is that unfortunately the 'inv' model is simply not
>> >> implemented yet. This is the model for the very old-school inversion
>> >> recovery type R1 experiments whereby the magnetisation returns to the
>> >> Boltzmann equilibrium. I'm guessing you should be using the 'exp'
>> >> model instead. This is the standard 2 parameter exponential fit
>> >> whereby the magnetisation goes to zero. This is the standard nowadays
>> >> as it is considered far more accurate for the extraction of the rates
>> >> (simply by having one less parameter to fit).
>> >>
>> >> If you have collected the old-school data, there is a relax branch
>> >> created by Sébastien Morin for handling this experiment type. This is
>> >> the 'inversion-recovery' branch located at
>> >> http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/.
>> >> However this branch is not complete and will require someone willing
>> >> to dive into C code to complete it (see
>> >> http://www.mail-archive.com/relax-devel@gna.o
Re: relaxation curve fitting
Hi,
This appears to be a unique bug! I would guess that it has something
to do with the software versions in use - on most systems this code
path works flawlessly. But I should be able to modify relax to handle
this. Would you be able to please make a bug report? The link is
https://gna.org/bugs/?func=additem&group=relax. If you could include
a short description, the error message, and the output of 'relax
--info', this would be of significant help. If possible, I would like
to try to catch this in the relax test suite. The more information
you provide the better - because if I can reproduce the problem on my
computer, I can then fix the problem within minutes. Otherwise it
takes much, much longer.
Cheers,
Edward
On 30 June 2012 21:16, Romel Bobby wrote:
> Hi Edward,
>
> I tried the 'exp' model and it gave me the very same error message (see
> below).
>
> File "/usr/local/relax/multi/processor.py", line 480, in run
> self.callback.init_master(self)
> File "/usr/local/relax/multi/__init__.py", line 319, in
> default_init_master
> self.master.run()
> File "/usr/local/relax/relax.py", line 183, in run
> self.interpreter.run(self.script_file)
> File "/usr/local/relax/prompt/interpreter.py", line 280, in run
> return run_script(intro=self.__intro_string, local=locals(),
> 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 570, 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 455, in
> interact_script
> exec_script(script_file, local)
> File "/usr/local/relax/prompt/interpreter.py", line 329, in exec_script
> runpy.run_module(module, globals)
> File
> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
> line 180, in run_module
> fname, loader, pkg_name)
> File
> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
> line 72, in _run_code
> exec code in run_globals
> File "/Users/b_romel/temp_relax/backup/relax_fit.py", line 87, in
> grid_search(inc=11)
> File "/usr/local/relax/prompt/uf_objects.py", line 220, in __call__
> self._backend(*new_args, **uf_kargs)
> File "/usr/local/relax/generic_fns/minimise.py", line 141, in grid_search
> grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
> verbosity=verbosity)
> File "/usr/local/relax/specific_fns/relax_fit.py", line 609, 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/relax_fit.py", line 716, in minimise
> if constraints and not match('^[Gg]rid', min_algor):
> File
> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/re.py",
> line 137, in match
> return _compile(pattern, flags).match(string)
> TypeError: bad argument type for built-in operation
>
> Regards,
>
> Romel
>
> On 1 July 2012 06:42, Edward d'Auvergne wrote:
>>
>> Hi Romel,
>>
>> The problem is that unfortunately the 'inv' model is simply not
>> implemented yet. This is the model for the very old-school inversion
>> recovery type R1 experiments whereby the magnetisation returns to the
>> Boltzmann equilibrium. I'm guessing you should be using the 'exp'
>> model instead. This is the standard 2 parameter exponential fit
>> whereby the magnetisation goes to zero. This is the standard nowadays
>> as it is considered far more accurate for the extraction of the rates
>> (simply by having one less parameter to fit).
>>
>> If you have collected the old-school data, there is a relax branch
>> created by Sébastien Morin for handling this experiment type. This is
>> the 'inversion-recovery' branch located at
>> http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/.
>> However this branch is not complete and will require someone willing
>> to dive into C code to complete it (see
>> http://www.mail-archive.com/relax-devel@gna.org/msg03353.html). Note
>> that if someone does know C, completing this will require about 50
>> lines of code changed in the maths_fns/relax_fit.c and
>> maths_fns/exponential.c files (my rough guess anyway). It should be
>> incredibly trivial for someone with C knowledge. Anyway, I hope some
>> of this info helps.
>>
>> Regards,
>>
>> Edward
>>
>>
>>
>> On 30 June 2012 18:01, Romel Bobby wrote:
>> > Dear all,
>> >
>> > I've been trying to use the curve fitting routine for R1 and R2 in relax
>> > using the sample script relax_fit.py. I managed to read in the spectra
>> > and
>> > obtain a value for the uncertainty. However, once it gets to the point
>> > of
>> > performing a grid_search that's where it fails (see below). Has anyone
>> > had a
>> > similar problem?
>> >
>> > [?1034h
