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