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. Thank you. alison
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@anl.gov -or- ravel@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/
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
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@anl.gov -or- ravel@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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participants (3)
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Alison Costello -
Alison L Costello
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Bruce Ravel