Hi Edward,
I upgraded everything to newest.
I tried to updated the script too, but when I run it I get this error
message:
File "/sw/lib/relax-py27/multi/processor.py", line 494, in run
self.callback.init_master(self)
File "/sw/lib/relax-py27/multi/__init__.py", line 318, in
default_init_master
self.master.run()
File "/sw/lib/relax-py27/relax.py", line 194, in run
self.interpreter.run(self.script_file)
File "/sw/lib/relax-py27/prompt/interpreter.py", line 275, in run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
File "/sw/lib/relax-py27/prompt/interpreter.py", line 578, in run_script
return console.interact(intro, local, script_file,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py27/prompt/interpreter.py", line 477, in
interact_script
exec_script(script_file, local)
File "/sw/lib/relax-py27/prompt/interpreter.py", line 352, in exec_script
runpy.run_module(module, globals)
File "/sw/lib/python2.7/runpy.py", line 180, in run_module
fname, loader, pkg_name)
File "/sw/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File
"/Users/andrasboeszoermenyi/relax-trunk/test_suite/shared_data/curve_fitting/saturation_recovery/relax_sym.py",
line 106, in <module>
minimise.grid_search(inc=11)
AttributeError: 'Uf_object' object has no attribute 'grid_search'
Not sure if that could be related to my recent upgrade to Yosemite, but I
think it shouldn't.
I uploaded the project as:
file #22996: saturation_recovery.tar.gz
Best,
Andras
________________________________________
From: edward.dauvergne@xxxxxxxxx [edward.dauvergne@xxxxxxxxx] On Behalf Of
Edward d'Auvergne [edward@xxxxxxxxxxxxx]
Sent: Thursday, November 27, 2014 1:16 PM
To: Boeszoermenyi, Andras
Cc: relax-devel@xxxxxxx; Sébastien M
Subject: Re: [sr #3195] Fitting of saturation recovery experiment
Hi Andras,
I have now included your files in relax
(http://article.gmane.org/gmane.science.nmr.relax.scm/24542). If you
have the trunk source code copy of relax and type:
$ svn up
You will see the files appear in the
test_suite/shared_data/curve_fitting/saturation_recovery directory.
If you could update your script for the latest relax version, I could
add it to the test_suite/system_tests/scripts/ directory. This would
then be very simple to set up as a system test by duplicating and
modifying this test:
http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_fit-pysrc.html#Relax_fit.test_zooming_grid_search
Cheers,
Edward
On 27 November 2014 at 19:06, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
wrote:
Hi Andras,
ok I uploaded a tar file with synthetic peaks for one spin system:
file #22989
Cheers! The permanent link to the file is
http://gna.org/task/download.php?file_id=22989, and this is attached
to the task #7415 (http://gna.org/task/?7415).
The saturation recovery formula is:
I0*(1 - exp(−R1*t))
The parameters I used were
I0 = 1000000000000000.00
and
R1 = 0.5
I'm wondering if this equation is correct. Should this not be:
I(t) = I_inf*(1 - exp(−R1*t))
Is the magnitisation not returning to the steady-state of I_inf? I
guess that in this experiment I0 == I_inf.
Obviously, the same numbers also work for the inversion recovery
experiment:
I(t) = I∞ − I0*exp(−R1*t)
with I∞ set to 1000000000000000.00 as well. Not sure how much that helps
though.
If I0 is set to something less than I_inf, this would give different
I(t) values. Such a data set could be used to implement the inversion
recovery experiment.
If "inv" is not implemented, then that would explain the weird results :)
More of a warning is probably required. Or a synthetic data set,
relax script, and system test created, and then this equation finally
implemented.
Unfortunately, I have no primary reference for the saturation recovery
experiment either.
It's a pity. The ancient primary references for all these basic and
old experiment types would be great for adding to the relax manual and
user function documentation. I can see that lots of people discuss
this older method, but I also don't see any references.
I was wondering if you were able to update to the latest version of
relax (3.3.3 at http://www.nmr-relax.com/download.html#Mac_OS_X), or
even better to use the relax trunk source code
(http://thread.gmane.org/gmane.science.nmr.relax.devel/3693/focus=7348).
Could you try to update the scripts to run with these versions? The
newest relax versions will tell you how the user functions have been
renamed.
Cheers,
Edward
Re: [sr #3195] Fitting of saturation recovery experiment