[Ifeffit] (no subject)

[Scott Calvin]

Hi MJacob,

One note that might help--it is not strictly necessary to fit the  
nearest-neighbors in order to fit the iron-iron path. In a system like  
this, I would think you might get lucky and have a big contribution  
from near-neighbors, then a bunch of smeared out stuff (as Matthew  
Marcus suggested) that effectively cancels, and then a little iron- 
iron peak because the iron is a much better scatterer than all the  
organics. If that's what the Fourier transform looks like, then you  
can fit from say 4 to 5 angstroms and just use an iron path. It sounds  
weird, but I've done things like that once or twice with decent  
results. There are certainly pitfalls; for instance I might be a  
little nervous about some focused MS path that happens to line up with  
the Fe-Fe distorting the results, but it's worth a shot.

--Scott Calvin
Sarah Lawrence College

Could you perhaps post an image of the Fourier transform of your data  
to the list? That would help give a sense of what might work and what  
wouldn't work.

On Mar 11, 2009, at 5:49 PM, Frenkel, Anatoly wrote:

> I would like to be proven wrong but my feeling is, without even  
> knowing anything about this particular system, that one cannot  
> observe Fe-Fe pair at that distance in such complex case.
> However, to approach it more rigorously, the first step would be to  
> examine the relative "importance" factors of different paths in the  
> output of FEFF. If Fe-Fe path is well isolated in distance and  
> importance from others (in reality, it probably is not the case) it  
> can be done, otherwise - not.
>
> Anatoly
>
>
> From: ifeffit-bounces at millenia.cars.aps.anl.gov <ifeffit-bounces at millenia.cars.aps.anl.gov 
> >
> To: ifeffit at millenia.cars.aps.anl.gov <ifeffit at millenia.cars.aps.anl.gov 
> >
> Sent: Wed Mar 11 09:40:31 2009
> Subject: [Ifeffit] (no subject)
>
> Hi all,
>
> I measured Fe(II) edge EXAFS data for my protein that has two iron  
> sites (Fe-Fe distance ~5A). My question is how to fit the model with  
> the data? Can I discard the contribution of multiple scattering  
> effects to the fitting? One most important information that I want  
> to obtain is on the Fe-Fe distance. Is it enough to conclude from  
> the raw data FT that the Fe-Fe  distance in my protein sample has  
> been changed in comparison to the Fe-Fe distance in the model  
> (created with Feff using the crystal structure coordinates)? I try  
> fitting using arthemis but got bad and weird results. is there any  
> manual or step-by step guide that I can learn how to fit model of  
> two metal sites to my data?
>
> Anther question that I have how can I get to the past discussions in  
> the forum- is there any database for questions and answers that I  
> can learn on the analysis of EXAFS data?
>
> Any help will be appreciated,
>
> MJacob
>
>  ars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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