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List:       relax-devel
Subject:    Re: Fit inversion-recovery R1 data
From:       "Edward d'Auvergne" <edward () domain ! hid>
Date:       2011-06-15 13:01:47
Message-ID: BANLkTinge9KRnogUXmfNdUO9c0PK_JpOJA () mail ! gmail ! com
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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@domain.hid> 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@domain.hid>  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
>
>


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