[Ifeffit] R-factor
vikrai at comcast.net
vikrai at comcast.net
Wed Jul 6 11:22:48 CDT 2005
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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