On Thursday 16 June 2005 21:09, Matt Newville wrote:

Hi Ann,

OS X 10.4 uses a new version of Perl which has some trouble with the Perl libraries that come bundled with Ifeffit.

The result seems to be that you have to build Perl/Tk for Perl 5.8.6. Rebuilding Perl/Tk is not too difficult, if you have the developer tools installed and have a passing familiarity with the unix-y parts of Darwin/OS X. The instructions at http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-May/001771.html

should help. If you try this, please let us know how it goes.

Sorry for the trouble. I don't have Tiger installed (and won't for at least two months, as vpn software that I need is known to not work with Tiger) and so cannot make a binary installer for it.

Could someone who has successfully built the software for 10.4 update the relevant FAQ entry? (http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=show&file=faq02.009.htp) Thanks, B -- Bruce Ravel ----------------------------------- bravel@anl.gov -or- ravel@phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (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/

Hello Scott, what about something on fitting spectra of disordered materials such as metalloproteins, having a quickly dying oscilaltion? A final word on the background removal, choice of kmin and kmax, and a protocol for fitting this kind of data would be very nice and welcome Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic 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 "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"

On Tuesday 21 June 2005 10:08, Stefano Ciurli wrote:

Dealing with the old question of background correction, I have several DIFFERENT recipes from SK and others. Especially the alignment of theory and experiment.

Is there anyone willing to give me a definitive protocol?

I should hope not! What works for a metallic alloy probably won't work for a uranyl. What works when you have 18 inverse angstroms of great data probably won't work when you have 9 of crappy data. To my mind, the important thing is to understand that Ifeffit treats the background in a Fourier sense. The background is that part of the mu(E) spectrum that contributes the low frequency components. What does "low" mean? That is the point of the Rbkg parameter in Athena and Autobk. Components below Rbkg are low and are the ones to be removed by the spline. Components above Rbkg are data and should not be removed by the spline. However, since the Fourier transform is finite, the separation between the frequency regimes is not strict. High components bleed into the low region and vice versa, resulting in correlations between the spline and the parameters that will be used to describe the data in Artemis. Similarly, when you do a background corefinement in Artemis, the spline is used to fit the Foruier components below Rmin and the feff paths are used to fit the components between Rmin and Rmax. The advantage offered by the background corefinement is that it allows you to approximately quantify the corellations bewteen the fitting parameters and the spline itself. So, I would say there is no definative protocol. There are certainly tricks that you can try in certain situations, even recipes you can follow in certain situations. But in every case, the bottom line is that you should understand that Ifeffit defines the background in a Fourier sense. If you understand that, there is very little else that should be mysterious in that part of the analysis.

In particular, SK writes that one should "read the data into Artemis": now, Artemis does not read the crude data and I have to go through Athena, as far as I understand. But when I read the athena.prj into Artemis, will the imported data be corrected already using the default values for the spline as provided in Athena? If so, there is already an initial bias, I think.

Disclaimer: I am going to speak to how things are done in the development version of Artemis. This is relevant since the next release of my codes will drop the 0.7 branch and the development branch and since the development branch will become the main, 0.8 branch. Artemis reads data and all the background removal parameters from the Athena project file. It then performs the background removal in the exact same way as in Athena and inserts that chi(k) into the project. So whatever decisions you made in Athena, those decisions get transplanted to Artemis. In the near future, there will be the possibility of tweaking the background removal from within Artemis. That will serve to close the loop that Shelly often describes in which she returns to Athena with new knowledge about the data, re-performs the background removal, then returns to the data analysis in Artemis. With this soon-to-come feature, the same loop will be possible, but it will be possible to do it entirely within Artemis. 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/