Re: Fit inversion-recovery R1 data -- June 15, 2011 - 15:02

Hi,

I would suggest a task for this and a new branch.  It should only take
a few days to implement.  Adding it to the GUI would also be quite
easy, we just need a selection box element to select between the 2
different equation types.  I have already implemented the following
for this type of analysis:

- the relax_fit.select_model() user function.

- all of the specific code for handling the additional 'iinf' parameter.

- the C code maths functions in maths_fns/relax_fit.c

The only thing missing is the code in math_fns/exponential.c as well
as a switch in maths_fns/relax_fit.c to select between the two
different curves (there would be other ways of implementing this
though).

Regards,

Edward



On 15 June 2011 14:49, Sébastien Morin <sebastien.morin@xxxxxxxxx> wrote:
> Hi,
>
> Thanks for your fast answer and for the explanation !
>
> Indeed (!), I know some people who record R1 in this manner in my
> (sometimes) very old-school lab...
>
> I guess we could implement this, at least for the command line version of
> relax, in case some people need it...
>
> Cheers,
>
>
> Séb  :)
>
>
> On 11-06-15 2:44 PM, Edward d'Auvergne wrote:
> > Hi,
> >
> > The inversion recovery method whereby the signals plateau at the
> > equilibrium I0 value is very old school.  I don't know if anyone
> > records this anymore.  Maybe some chemists do.  Anyway, I never added
> > support for this because no one was interested or had such data.  The
> > new interleaved method resulting in a single exponential from I0 to
> > zero is much better, in that the results are much more reliable.  The
> > signals affected by noise are at the end of the exponential rather
> > than in the middle.  And the 2 parameter fit is much more reliable for
> > extracting the rate.  This is all explained in the original paper, but
> > I can't remember the reference off the top of my head.  It should be
> > referenced in the Farrow 94 paper though, which is the basic reference
> > for all R1, R2, and NOE experiments nowadays.
> >
> > Support could easily be added to relax for this.  I actually have
> > coded the relax_fit analysis to support the triple parameter fit
> > curve, but never implemented it.  Do you know someone who has measured
> > the R1 in this way?
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> > On 15 June 2011 14:35, Sébastien Morin<sebastien.morin@xxxxxxxxx>  wrote:
> > > Hi,
> > >
> > > Talking with some colleagues, I realized that some people record R1 data
> > > with 2D versions of inversion-recovery pulse sequences, where the signal
> > > starts from a negative value to a positive value, with a cross-point at ~
> > > ln
> > > 2 / R1. The equation needed to fit such data is the following:
> > >    At = A0 (1-2e^(-R1 t))
> > >
> > > In relax (and relaxgui), it is assumed that, for both R1 and R2, the user
> > > records data with intensities decaying in an exponential manner (i.e. At
> > > =
> > > A0 e^(-R1 t) ).
> > >
> > > Is there a reason why most people use the exponential decay approach,
> > > rather
> > > than the inversion-recovery approach ?
> > >
> > > Should relax (and relaxgui) support the inversion-recovery approach ?
> > >
> > > Cheers,
> > >
> > >
> > > Séb  :)
> > >
> > > --
> > > Sébastien Morin, Ph.D.
> > > Postdoctoral Fellow, S. Grzesiek NMR Laboratory
> > > Department of Structural Biology
> > > Biozentrum, Universität Basel
> > > Klingelbergstrasse 70
> > > 4056 Basel
> > > Switzerland
> > >
> > >
> > > _______________________________________________
> > > relax (http://nmr-relax.com)
> > >
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> --
> Sébastien Morin, Ph.D.
> Postdoctoral Fellow, S. Grzesiek NMR Laboratory
> Department of Structural Biology
> Biozentrum, Universität Basel
> Klingelbergstrasse 70
> 4056 Basel
> Switzerland