[Ifeffit] R-factor

[vikrai at comcast.net]

Alison,
I don't think that the difference of R-factors you mention is a big deal. You did not mention in your message more important thing. Did you get the same values of parameters? Besides, it is hardly to expect to find a signal caused by photoelectron backscattering at R<1 A. So the lower limit in R-space fitting equal to 0.1 A is too small probably. As well as the lower limit in q-space fitting because in proteins in this momentum region only full multiple scattering approach should work correct.
Victor Krayzman
-------------- Original message -------------- 

> Bruce, 
> 
> I've looked, and my R-factors for the back-transformed 
> space are not necessarily twice the value of the R-factors 
> for the k-space fits. In fact, they are often quite 
> close. For example, just recently I had a k-space 
> R-factor of 0.102 and a q-space R-factor of 0.113. Now, I 
> realize those numbers are very close, but I'm afraid if I 
> try to publish this, then I will get criticism for the 
> q-space R-factors being larger. If I can explain it, then 
> maybe it won't be a problem. 
> 
> I do see what you're saying about the complex vs. real 
> function, and that definately makes sense, but they don't 
> differ by a factor of 2. Hmmm. 
> 
> alison 
> 
> On Wed, 6 Jul 2005 09:43:03 -0500 
> Bruce Ravel wrote: 
> > On Tuesday 05 July 2005 18:39, Alison Costello wrote: 
> >> I have a question regarding the calculation of the 
> >>R-factor. I am 
> >> currently using SIXPACK to process my protein EXAFS 
> >>data, and I fit the 
> >> data in both k-space and in q-space (back-transformed 
> >>k-space). I 
> >> typically will use k-ranges = [1-13.6] and for 
> >>multiple-scattering fits, 
> >> will use an R-range of 0.1 - 4.5. Sometimes, the 
> >>R-factor for the q-space 
> >> fit is greater than the R-factor for the k-space fit, 
> >>which should not be 
> >> true, as the back-transformed space filters out noise. 
> >> I am confused as to 
> >> why this occurs, and am wondering if the R-factor for 
> >>the back-transformed 
> >> space is calculated differently than for k-space fits. 
> > 
> > Alison, 
> > 
> > I would expect the R factor to be bigger in k space due 
> >to the high frequency 
> > portions of the data that get filtered out of the q 
> >space data. That is what 
> > happened in the one example I just tried. 
> > 
> > What are some example values of the R-factors? Do they 
> >differ by about a 
> > factor of 2? 
> > 
> > One thing that occurs to me is that chi(q) is a complex 
> >function while chi(k) 
> > is a real function. In Ifeffit those two functions 
> >should have the same 
> > number of points, but the R factor in q is computed 
> >using both parts of the 
> > complex function. Thus it would seem reasonable if they 
> >differed by about 2 
> > and there were no significant Fourier components in the 
> >data beyond your rmax. 
> > 
> > B 
> > 
> > -- 
> > Bruce Ravel ----------------------------------- 
> >bravel at anl.gov -or- 
> > ravel at phys.washington.edu 
> > Environmental Research Division, Building 203, Room 
> >E-165 
> > Argonne National Laboratory 
> > phone: (1) 630 252 5033 
> > Argonne IL 60439, USA 
> > fax: (1) 630 252 9793 
> > 
> > My homepage: http://feff.phys.washington.edu/~ravel 
> > EXAFS software: 
> >http://feff.phys.washington.edu/~ravel/software/exafs/ 
> > 
> > _______________________________________________ 
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