[Ifeffit] Autobk parameters

Wed May 26 07:26:20 CDT 2004

Hi folks,

I have some questions that for most of you are certainly trivial, but 
for a newcomer trying to learn things by himself are not, so please 
bear with me. I am trying to figure out the BEST parameters for 
Athena processing of a set of spectra recorded on Ni and Zn protein 
samples, therefore dealing with spectra containing disorder and fast 
dying signal, also with some degree of noise.

I figure that in order to run the fitting I need to start from data 
whose processing I trust. I also figure that the data will look 
differently (obviously) dependign on the parameters I use for the 
processing with Athena, so I will try to address some points here. I 
hope someone has some time to answer:

1) I understand that energy calibration should be performed, and I 
did so by using the atomic edge energy. I also understand that this 
parameter could be fluctuating in the subsequent fitting. Any comment 
on this procedure?

2) The next parameter is Rbkg. I have read the literature about this 
parameter, especially the 1993  paper by Matt. I sort of understood 
the rationale and method, but I also gathered that the default 
parameter of 1.0 can be changed. What are the criteria for changing 
this? I tend to keep it to the default value, but I feel a bit uneasy 
about not being able to control this parameter intelligently.

3) I understood from the paper by Matt (and from the "Using Athena" 
manual by Bruce) that one could use a "standard" to estimate the 
level of leakage into the small chi(R) region (apodization effects 
due to Fourier window filtering). The manual states that one can read 
in a chi.dat file produced with feff. However, I do not understand 
how to build the feff.inp for feff and produce a useful chi.dat to 
use as a "standard". Please help?

4) Then there is the k-weight parameter to be changed for the 
background removal. The default value for this is 1, but higher 
values are allowed. I noticed that increasing the k-weight for 
background removal produces a curve in the chi(E) which more and more 
appear to disregard the edge peak, resembling more and more a 
smoothly monotonically increasing curve. Consequently, the chi(k) 
changes depending on this parameter, and I again start to be worried 
about the following fit of it. What are the criteria to choose this 
k-weight for the background?

5) The Pre-edge range: here the manual (and the online help) states 
that the range is -200 to - <snip> (btw, is there a way to see the 
end of the long sentences in the echo area?) but the actual default 
values are -150/-75 for most cases, while it can be different for 
different spectra. I do not understand the rationale in choosing 
these default values. I am guessing that the program somehow finds 
the "best" range and uses it. If so, i would like to know the 
criteria for this choice. Also, I read somewhere in your documents 
that one should try to have the pre-edge and the post-edge lines to 
run parallel. Is this a good criterium? Should I change the pre- and 
post-edge ranges in order to satisfy this criterium? If the default 
values yield non-parallel lines should I worry? If so, what should I 
do?

6) Spline range: this is another important issue, I think. In the 
paper by Matt it is stated that "standard practice ... has been to 
ignore everything below an energy typically 30 eV above the E0" and 
that Autobk is an advantage because it can read in data very close to 
the E0. My question is: the default value for k in the spline range 
is set to 0.5 eV (0.952 eV). What are the criteria to change this 
default value? Also, is there any relationship between this range and 
the range subsequently used for FT? My guess is that the k-min for FT 
should be always higher that the k-min for the spline range, but 
please comment on this.  Also, what are the criteria to set the 
default value for k-max in the background removal spline? Does this 
relate to k-max for FT in the sense that the latter should always be 
smaller than k-max used for spline background calculation? I also 
noticed that (obviously) the peak in the chi(R) spectrum which is at 
R values smaller than the first shell coordination distance decreases 
as I increase the k-min for the spline calculation, while the first 
and more distant shells are less influenced by this parameter (even 
though to a significant extent, which, again, worries me). What is 
the best value for k-min for the spline and what are the criteria for 
deciding?

7) for the FT parameters: Shelly's protocol to define the k-range to 
best calculate the chi(R) was clear and useful to me. However, I 
would like to know more about choosing the dk parameter and the 
window-type. I need some general criteria to choose between the 
various possibilities.  I noticed that the kaiser-bessel window is 
the default, but in the literature I almost invariably find the 
Hanning window. Please comment.

I come from the NMR spectroscopy world, and I am used to run FT and 
play around with the parameters defining the type of apodization 
function. However, in that case, it was pretty clear to me what are 
the standard parameters used by most people, while here, being new to 
the game, I need some guidance. I tried to read all the material 
available (thanks a lot for such a great effort) and also the 
previous mailing list messages, but I thought that it was time to ask 
al the questions I have at once.
I feel like a naive cook who is afraid of making mistakes, and 
therefore reads a receipe very carefully, not to mix the wrong 
ingredients in the wrong amounts. So, again, please bear with me.

Best,
Stefano
-- 
____________________________________________

Stefano Ciurli
Professor of Chemistry
Department of Agro-Environmental Science and Technology
University of Bologna
Viale Giuseppe Fanin, 40
I-40127 Bologna
Italy
Phone:	+39-051-209-6204
Fax: 	+39-051-209-6203

"Fatti non foste a viver come bruti,
ma per seguir virtute e canoscenza"
Dante Alighieri - Inferno - Canto XXVI