[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! :)


  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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