Re: [sr #3195] Fitting of saturation recovery experiment -- November 27, 2014 - 19:16

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