[Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples
Bruce Ravel
bravel at bnl.gov
Thu Nov 12 16:55:31 CST 2015
On 11/10/2015 05:54 PM, Carolyn Carr wrote:
> Thanks so much for clarifying that for me! I have been basing my fitting
> in R-space off of
>
> XAFS spectroscopy; fundamental principles and data analysis DOI
> 10.1023/A:1019105310221
>
> which has a section on fitting in R-space over k-space although it is
> very possible I misinterpreted its analysis.
Hi Carolyn,
I believe you are referring to the text at the top left of page 150 in
that paper.
Those authors say a number of things differently from how I would say
them, however, there is one line that is certainly not relevant to how
we do the analysis in Artemis and Ifeffit (or Artemis and Larch). The
fitting metric in R space is evaluated using the real and imaginary
parts of the complex Fourier transform. Thus, the bit at the end of
that paragraph does not relate to our software.
It been a long time (possibly decades!) since I have looked into the
possibility of fitting magnitude and phase instead. My vague memory is
that Matt found that using real/imaginary was more stable in Ifeffit.
In any case, the point in that paper is not valid for our software
because we use oscillatory functions when fitting in k, R, or
back-transform k space.
I think that helps put my earlier comment into proper context for you.
Wonderful post, though! It is very pleasant to see a post that doesn't
involve someone complaining about something related to the Mac! :)
Cheers,
B
--
Bruce Ravel ------------------------------------ bravel at bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage: http://bruceravel.github.io/home/
Software: https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
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