New Method for Normalization?
XANES Aficionados, I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features. Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below: J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines? Dave _________________________________ David Barton The Dow Chemical Company
On Thursday 29 September 2005 15:48, Barton, David (DG) wrote:
Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below:
J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn
It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines?
Isn't Ifeffit's Cromer-Liberman normalization scheme substantially similar to the method presented in that paper? B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Hi Dave, Thanks for bringing this up. I've talked with Tsu-Chien about the MBACK procedure discussed in the JSR article, and about whether he thought it would be worth adding to Ifeffit. I interpreted our conversation to be that it wasn't a very high priority for either of us two to do the implementation soon. (I don't recall if Tsu-Chien is on this list, but I'd be happy to be corrected). I do not mean to say that I think it should not be done. I do think the Cromer-Libermann background (bkg_cl) command in ifeffit is sort of close, but it does ignore any drifts in instrumentation response. And Ifeffit always does a linear pre-edge. I've come to understand (especially from people with very dilute samples and solid state detectors) that this can be a noticeable problem. I think including the MBACK approach is a good idea, and would not want to discourage anyone from making that happen. But having an option for a Victoreen pre-edge, say, is probably even more important. I think that coupling a better pre-edge function with the Cromer-Libermann background might get 3/4 of the way to the MBACK approach. I'd love to hear other opinions on this.... --Matt On Thu, 29 Sep 2005, Barton, David (DG) wrote:
XANES Aficionados,
I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features.
Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below:
J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn
It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines?
Dave _________________________________ David Barton The Dow Chemical Company
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Bruce and others, Back in the day, I used to use a "trick" for generating feff files for non-crystalline, molecular substances (or small nanoclusters). I'd use a space group of P 1 with a = b = c = 100, and alpha = beta = gamma = 90...then I could enter coordinates in hundredths of an Angstrom. But I tried the trick recently, and the Atoms inside Artemis complains that I should be using a cubic space group and doesn't run. I don't know my space groups very well, but is there actually a cubic group that doesn't have any symmetry within the unit cell? It seems to me that a real material (not just my trick) could have an "accidentally" cubic unit cell without being a cubic space group. Can someone who knows crystallography better than I do confirm that? If so, then atoms could issue a warning, but should not prevent a feff.inp file from being generated. Incidentally, of course I know there's a fairly trivial alternative to my trick...I could just create the feff.inp file without using atoms (Artemis even conveniently provides a template). But I think it's marginally easier for some of those new to the software to use the P 1 method, because then they don't have to think about potential lists and such. --Scott Calvin Sarah Lawrence College
Hi Scott, For molecular substances, the accuracy in atomic coordinates that are obtained by one of the three most popular methods (e.g., in Protein Data Bank, the sources are X-ray crystallography, solution NMR, or theoretical modeling, here is a good review: http://www.rcsb.org/pdb/experimental_methods.html) is much worse than 0.1 A. I got this number assuming the resolution of 1 A (considered high for a protein, see the link above, and estimating the uncertainty of the position of an atom as roughly one tenth of the resolution, again using the quote from the same article. Thus, in such protein, x-ray crystallography would not guarantee atomic positions with better than 0.1 A accuracy. Resolution provided by solution NMR is "not as detailed and accurate as that obtained crystallographically" - the quote from the same source. Therefore, for all purposes, creating a pseudo cubic cell will halp: choose lattice parameters 99.9, 100 and 100.1. This will introduce 0.1% error in the distances that are obtained by Atoms for such P1 unit cell compared to those obtained by Atoms for a cubic cell. This 0.1% error in distances is negligible for all purposes. I am not sure Atoms will allow the lattice parameters to be that close but I do not see why it should not. Anatoly -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of scalvin@slc.edu Sent: Sunday, October 02, 2005 11:32 AM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] P 1 space group Hi Bruce and others, Back in the day, I used to use a "trick" for generating feff files for non-crystalline, molecular substances (or small nanoclusters). I'd use a space group of P 1 with a = b = c = 100, and alpha = beta = gamma = 90...then I could enter coordinates in hundredths of an Angstrom. But I tried the trick recently, and the Atoms inside Artemis complains that I should be using a cubic space group and doesn't run. I don't know my space groups very well, but is there actually a cubic group that doesn't have any symmetry within the unit cell? It seems to me that a real material (not just my trick) could have an "accidentally" cubic unit cell without being a cubic space group. Can someone who knows crystallography better than I do confirm that? If so, then atoms could issue a warning, but should not prevent a feff.inp file from being generated. Incidentally, of course I know there's a fairly trivial alternative to my trick...I could just create the feff.inp file without using atoms (Artemis even conveniently provides a template). But I think it's marginally easier for some of those new to the software to use the P 1 method, because then they don't have to think about potential lists and such. --Scott Calvin Sarah Lawrence College _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Anatoly, I agree that a) it's unfortunate that Artemis is too clever in noticing that a P1 space group has some symmetry and prevents the Feff calculation when this happens. I'd suggest a space group called 'Cluster' or 'Molecule' or something that would indicate that there should be no space filling procedures done, and that all atoms in the molecule/cluster are specified, but still let you enter atomic coordinates as relative to a 'lattice constant'. It is possible to just enter the xyz coords in the feff.inp, but Atoms/Artemis does such a nice job at filling out the rest of feff.inp that using a P1-like space group is a very convenient choice. b) using a = 99.9, b=100.0, c=100.1 is a good way to fool Artemis/Atoms.
For molecular substances, the accuracy in atomic coordinates that are obtained by one of the three most popular methods (e.g., in Protein Data Bank, the sources are X-ray crystallography, solution NMR, or theoretical modeling, here is a good review: http://www.rcsb.org/pdb/experimental_methods.html) is much worse than 0.1 A.
That seems a little unfair. Certainly most macromolecular (>5kD) diffraction data as is typically found in the PDB often has a resolution worse than 1A. But powder diffraction measurements and theoretical modeling of crystallized small molecules (and the definition of 'small' seems to be growing) and clusters often have precisions better than 0.01A. If 0.1A really were the accuracy needed, then you could use a = 90, b=100, c=110 in your example. That would give a very noticeable difference in any decent powder diffraction data and in the EXAFS. OTOH, using '99.9, 100.0, 100.1' would be more challenging to see with powder diffraction and very difficult to see with EXAFS. In both cases, the distances could easily be refined from that "off by 0.1%" starting point. For EXAFS at least, the same would not be true if the starting distances were off by 10%. Anyway, paraphrasing Juraj's suggestion, using '99.99, 100.00, 100.01' will certainly be OK and is not any harder to type than '90, 100, 110'. --Matt
Scott, I use a P1 cell with parameters a=10.0001 b=10.0002 c=10.0003 alpha=90.001 beta=90.002 gamma=90.003 with no complaints. There is no cubic group with no symmetry (actually, every space group has some symmetry elements, for P1 it's only one - identity). It is theoretically possible to have a unit cell with 'cubic-like' parameters and triclinic symmetry, but quite unlikely. However, some people like that idea. There was a paper which proposed a triclinic symmetry and pseudocubic cell for pyrite to explain the anomalous anisotropy of pyrite in reflected light. So there you have it. Juro On Sun, 2 Oct 2005 11:31:30 -0400 (EDT) scalvin@slc.edu wrote:
Hi Bruce and others,
Back in the day, I used to use a "trick" for generating feff files for non-crystalline, molecular substances (or small nanoclusters). I'd use a space group of P 1 with a = b = c = 100, and alpha = beta = gamma = 90...then I could enter coordinates in hundredths of an Angstrom.
But I tried the trick recently, and the Atoms inside Artemis complains that I should be using a cubic space group and doesn't run.
I don't know my space groups very well, but is there actually a cubic group that doesn't have any symmetry within the unit cell? It seems to me that a real material (not just my trick) could have an "accidentally" cubic unit cell without being a cubic space group. Can someone who knows crystallography better than I do confirm that?
If so, then atoms could issue a warning, but should not prevent a feff.inp file from being generated.
Incidentally, of course I know there's a fairly trivial alternative to my trick...I could just create the feff.inp file without using atoms (Artemis even conveniently provides a template). But I think it's marginally easier for some of those new to the software to use the P 1 method, because then they don't have to think about potential lists and such.
--Scott Calvin Sarah Lawrence College
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
---------------------------------- Juraj Majzlan Institute of Mineralogy and Petrology Albert-Ludwig-University of Freiburg Albertstrasse 23b Freiburg, D-79104, Germany telephone +49-761-203-6416 fax +49-761-203-6407 http://www.minpet.uni-freiburg.de/sites/personen/majzlan.html
Hi all, So there are clearly quite a few of these who use this trick, and the common work-around of using not quite cubic parameters suggests to me that Atoms should preferentially not be fighting us on this one. When you have time, Bruce, is it possible to make it so that Atoms doesn't prevent P1 having a=b=c and alpha=beta=gamma=90 (maybe just a warning)? Alternatively, Rick Reeder suggested a "molecular" option on the Atoms page that turns off the periodicity altogether and just lets users enter coordinates in angstroms. This is low-priority stuff, of course, since there are multiple simple work-arounds available. --Scott Calvin Sarah Lawrence College
Scott,
I use a P1 cell with parameters a=10.0001 b=10.0002 c=10.0003 alpha=90.001 beta=90.002 gamma=90.003 with no complaints.
Hi all, I've added a user page for me on the Ifeffit wiki, and started a list of tips for analyzing materials that aren't perfect crystals...that's one of the more common questions I get from beginners at workshops or whatever, and it seemed worth having. I've got a little bit on amorphous materials and substitutionally doped materials right now, and plan to add sections on macromolecules and nanoparticles. Feel free to add to (or edit!) the list. Aside from being linked from my user page, I also linked it to the XAFS analysis page. --Scott Calvin Sarah Lawrence College
Thanks Scott, That should be very useful! Maybe there coulld be a page on 'P1 tricks'??? --Matt
Matt said:
Maybe there coulld be a page on 'P1 tricks'???
Absolutely--that's what inspired me to ask the question today. I was about to put a page for "Macromolecular," giving the P 1 trick, when I found that following the advice I just gave at the NSLS EXAFS course didn't actually work. :( I'll add that page soon, once I'm sure the conversation on the topic has converged... --Scott Calvin Sarah Lawrence College
Hi, Over the weekend while I was out of town, there was an interesting discussion anout the strange things people do with Atoms to generate feff.inp files from lists of atomic coordinates. Some of the discussion centered around some sort of "molecule mode" which, frankly, I'm not sure I understand. I am curious what kinds of structural data people are converting to feff.inp form using the odd-ball techniques that Scott, Juraj, and Anatoly mentioned. Are you using data in the form of the Protein Data Bank? If your data comes from other sources, can you tell me which sources. The reason I'd like to know what resources people are using for their structural data is that I feel I can write a better tool for doing this if I know more about where the data is coming from. For instance, Protein Data Bank files have a specific grammer associated with them. That makes it a lot easier to write an intelligent tool that will generate feff.inp files that are correct. To my mind, a tool that attempts to generate feff.inp files from arbitarily formatted lists of atomic coordinates will likely be fragile in the sense that it will require considerable intervention by the user. So, I would like to hear from your folks about where you get your non-crystallographic structural information. The more input I get, the more likely that a truly useful tool can be incorporated into Artemis. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Hi Bruce, I can recall two cases where I've done this: I used Hyperchem to model some small molecules (butyl bromides for a gas-phase study). I constructed the coordinates for an icosahedral nanocluster by hand. --Scott Calvin Sarah Lawrence College At 06:57 PM 10/3/2005 -0500, you wrote:
So, I would like to hear from your folks about where you get your non-crystallographic structural information. The more input I get, the more likely that a truly useful tool can be incorporated into Artemis.
Dear Subscribers, May I ask you do me a big favor to let me know when plan EXAFS experiment for comparison of local structural enviroments around certain say, Cu atoms, how to evaluate the accuracy in term of atomic spacing in angstroms for instance? secondly, if if have knowledge of European based EXAFS source, could you suggest which stations may allow the user to have sample envrioement to do in-situ measurement? best regards, Ling fei
On Friday 04 November 2005 16:23, Ling Fei Zhang wrote:
May I ask you do me a big favor to let me know when plan EXAFS experiment for comparison of local structural enviroments around certain say, Cu atoms, how to evaluate the accuracy in term of atomic spacing in angstroms for instance?
It's possible I don't quite understand your question, but.... I'll give it a try. In any experiment that relies heavily upon theory and upon non-linear minimization (EXAFS certainly falls in that category, as do lots of other measurement techniques), one is wise to question accuracy. To my mind, the only way to satisfy oneself is to test the analytical apparatus against a well known standard. To use your example, you could test your theory and analysis software with copper metal and copper oxide. Let's assume that you can do the analysis on the standards and obtain good fits with physically reasonable parameters. If the interatomic distances then match what is known from, say, diffraction within the reported error bars, then you can have some confidence in the accuracy of the analytical apparatus. What I described is exactly what those of us who write this stuff do with our codes as we develop them. The codes must give answers to questions for which we know the answer before we can trust the answers to questions for which the answer is previously unknown. Of course convincing yourself of accuracy in the case of an unknown -- almost all research problems are unknown, that's why they are research problems! -- can be daunting. There are all sorts of empirical and modeling errors which can have an impact on the accuracy of a measurement. Such concerns have to be addressed for each individual analysis problem. But certainly knowing that the codes work on the standards is a good place to start. HTH, B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Dear Ling Fei, since the combination of XAFS with in-situ measuremnets is one of the most important applications of XAFS spectroscopy you will find more or less well equipped facilities at any synchrotron that operates XAFs beamlines. I suggest you have a look at the different synchrotron's web pages. And coming from Hamburg I suggest you start at: http://www-hasylab.desy.de/ Look especially for the beamlines X1 and E4. You will also find links to other synchrotron radiation facilities. Alternatively you are welcome to contact me via my e-mail adress. Best regards, Edmund Welter Ling Fei Zhang wrote:
secondly, if if have knowledge of European based EXAFS source, could you suggest which stations may allow the user to have sample envrioement to do in-situ measurement?
-- Dr. Edmund Welter HASYLAB at DESY e-mail : edmund.welter@desy.de Notkestr. 85 fon : (+49)-40-8998-4510 D-22603 HAMBURG fax : -2787 GERMANY secretary : -2304
Hello XAFS community, A while ago I wrote asking about how to read the Farrel Lytle Database and I get a pretty nice reply of Matt with the Ifeffit FAQ on "How to read the Farrel Lytle database" :P (I forgot to read that before asking!!) However the FL database have several file headers, like the following; CUEDGE START STOP BEG FSCTS: 168620. 176900. 142200. 2000. 5. DELTA: 200. 10. 40. 80. 0. DELEND: 169600. 167600. 159300. 142200. 0. SEC: 1. 1. 2. 3. 1. I figure that the values first line values are still motor steps, but is there a sort of "known" dspace and step/deg value for these cases?. Maybe I'm in other edge? Any help is most welcome Regards, Marco
On Monday 07 November 2005 20:36, marco antoni alsina corvalan wrote:
Hello XAFS community,
A while ago I wrote asking about how to read the Farrel Lytle Database and I get a pretty nice reply of Matt with the Ifeffit FAQ on "How to read the Farrel Lytle database" :P (I forgot to read that before asking!!) However the FL database have several file headers, like the following;
CUEDGE START STOP BEG FSCTS: 168620. 176900. 142200. 2000. 5. DELTA: 200. 10. 40. 80. 0. DELEND: 169600. 167600. 159300. 142200. 0. SEC: 1. 1. 2. 3. 1.
I figure that the values first line values are still motor steps, but is there a sort of "known" dspace and step/deg value for these cases?. Maybe I'm in other edge? Any help is most welcome
I have no idea, but you could certainly try using the d-spacings for Si111, Si311, and Si220. There aren't all that many kinds of crystals commonly used in XAS. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/
Marco,
A while ago I wrote asking about how to read the Farrel Lytle Database and I get a pretty nice reply of Matt with the Ifeffit FAQ on "How to read the Farrel Lytle database" :P (I forgot to read that before asking!!) However the FL database have several file headers, like the following;
CUEDGE START STOP BEG FSCTS: 168620. 176900. 142200. 2000. 5. DELTA: 200. 10. 40. 80. 0. DELEND: 169600. 167600. 159300. 142200. 0. SEC: 1. 1. 2. 3. 1.
I figure that the values first line values are still motor steps, but is there a sort of "known" dspace and step/deg value for these cases?. Maybe I'm in other edge?
Yes, there are a few different formats of data in the Lytle database. As far as I can tell, the files with 'CUEDGE START STOP BEG FSCTS: ...' do not include a "known" d-spacing or steps-per-degree, but tend to use Si(111) (dspace = 1.9202). You didn't include the rest of the file or say which file you're trying to use, so it's impossible to tell what problem you're having. Many of the files like this in the Lytle database also have data layed out in a fairly strange way, with steps,mu in pairs but 4 to a line. These have to be read with a 'narrays=2' argument to read_data(). Such files can usually be read with this macro: # read Farrel Lytle data file, convert to mu(E) macro read_lytle file group 4000 " Read some Lytle datafiles : filename groupname steps-per-degree" read_data ($1, group=$2, narrays=2) set (dspace = 1.92017, stpdeg = $3) set (r2d = 57.29577951, hc = 12398.61) set $2.energy = hc / (2 * dspace) / sin($2.1 / (r2d * stpdeg)) set $2.xmu = $2.2 end macro with 'steps-per-degree' usually either 4000, 8000, or 16000, and used as in: Ifeffit> read_lytle cuzno.012 cuzno 8000 You may have to play with it some. If that doesn't help, please ask a more specific question. --Matt
Bruce,
I also make up the structural models 'by hand' - taking
polyhedra and turning them around. That's why I use the
space group P1.
Juro
On Mon, 3 Oct 2005 18:57:33 -0500
Bruce Ravel
Hi,
Over the weekend while I was out of town, there was an interesting discussion anout the strange things people do with Atoms to generate feff.inp files from lists of atomic coordinates. Some of the discussion centered around some sort of "molecule mode" which, frankly, I'm not sure I understand.
I am curious what kinds of structural data people are converting to feff.inp form using the odd-ball techniques that Scott, Juraj, and Anatoly mentioned. Are you using data in the form of the Protein Data Bank? If your data comes from other sources, can you tell me which sources.
The reason I'd like to know what resources people are using for their structural data is that I feel I can write a better tool for doing this if I know more about where the data is coming from. For instance, Protein Data Bank files have a specific grammer associated with them. That makes it a lot easier to write an intelligent tool that will generate feff.inp files that are correct. To my mind, a tool that attempts to generate feff.inp files from arbitarily formatted lists of atomic coordinates will likely be fragile in the sense that it will require considerable intervention by the user.
So, I would like to hear from your folks about where you get your non-crystallographic structural information. The more input I get, the more likely that a truly useful tool can be incorporated into Artemis.
B
-- Bruce Ravel ---------------------------------------------- bravel@anl.gov
Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007
Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793
My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
---------------------------------- Juraj Majzlan Institute of Mineralogy and Petrology Albert-Ludwig-University of Freiburg Albertstrasse 23b Freiburg, D-79104, Germany telephone +49-761-203-6416 fax +49-761-203-6407 http://www.minpet.uni-freiburg.de/sites/personen/majzlan.html
Hi, Dave and Matt, Sorry for late reply. I was attending a workshop at ALS last week. The conventional way for EXAFS scaling is to extrapolate the spline to the "edge energy" and set this pre-edge-background-free value as 1.0. chi(k) = [ mu(E) - mu0(E) ] / mu0(E) ~ [ mu(E) - mu_bkg(E) ] / mu_bkg(E) ~ [ mu(E) - mu_bkg(E) ] / mu_bkg(E0) where mu_bkg(E0) gives an edge jummp of one For transmission XAS data, using Victoreen or 2nd-order polynomials as background functions have been sufficient to give correct EXAFS for two decades. Since EXAFS is the fraction modulation in the absorption coefficient, improper EXAFS scaling might lead to different EXAFS fitting results. In few cases, this could be a problem. I could think of two scenarios: 1) fluorescence XAS data for dilute samples and 2) XAS has a large intensity in the principle peak, eg. lanthanides. In scenario 1, using a linear function to fit a large and curved pre- edge background would result in different EXAFS scaling. In scenario 2, the intensive peak would heavily affect the curvature of the spline and make it difficult to define a unique edge jump. We have XAS spectra for duplicate protein samples measured in two beamlines. Using stepwise normalization (pre-edge + post-edge), one gives ZnS4 and another gives ZnS3O while the x-ray crystal structure shows it's a ZnS4 site. If we use a conjunctional background (MBACK), both give ZnS4. I don't have any example for the scenario 2, but I have used MACK to normalize Gd L3/L3/L1-edges simultaneously and show the two Gd conformers have slightly different intensity in L3 peak and not in L2/ L1. I agree with Matt that bkg_() plus a better pre-edge background could perform the way as what MBACK does. The main application of MBACK would be XANES analysis. It's kind of irritating to see people normalize peak height to compare the edge shift in Mn or Fe. Tsu-Chien <Chien>001000</Chien> On Sep 29, 2005, at 5:00 PM, Matt Newville wrote:
Hi Dave,
Thanks for bringing this up. I've talked with Tsu-Chien about the MBACK procedure discussed in the JSR article, and about whether he thought it would be worth adding to Ifeffit. I interpreted our conversation to be that it wasn't a very high priority for either of us two to do the implementation soon. (I don't recall if Tsu-Chien is on this list, but I'd be happy to be corrected).
I do not mean to say that I think it should not be done. I do think the Cromer-Libermann background (bkg_cl) command in ifeffit is sort of close, but it does ignore any drifts in instrumentation response. And Ifeffit always does a linear pre-edge. I've come to understand (especially from people with very dilute samples and solid state detectors) that this can be a noticeable problem.
I think including the MBACK approach is a good idea, and would not want to discourage anyone from making that happen. But having an option for a Victoreen pre-edge, say, is probably even more important. I think that coupling a better pre-edge function with the Cromer-Libermann background might get 3/4 of the way to the MBACK approach.
I'd love to hear other opinions on this....
--Matt
On Thu, 29 Sep 2005, Barton, David (DG) wrote:
XANES Aficionados,
I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features.
Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below:
J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/ S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn
It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines?
Dave _________________________________ David Barton The Dow Chemical Company
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Dear Dr. Weng, My name is Van Vu, a grad student in Larry Que's group, Department of Chemistry at University of Minnesota. We are using XAS to characterize the active site of mono and diiron enzymes, as well as model complexes. Normalization is a critical step of our XAS analysis. It would be highly appreciated if I can get a copy of MBACK program from you. Thank you very much. Best regards, Van Vu
Hi all, Please ignore this email since I mistakenly sent it to this mailing list. Thanks. Van Van Vu wrote:
Dear Dr. Weng, My name is Van Vu, a grad student in Larry Que's group, Department of Chemistry at University of Minnesota. We are using XAS to characterize the active site of mono and diiron enzymes, as well as model complexes. Normalization is a critical step of our XAS analysis. It would be highly appreciated if I can get a copy of MBACK program from you. Thank you very much. Best regards, Van Vu _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (12)
-
Anatoly Frenkel -
Barton, David (DG) -
Bruce Ravel -
Edmund Welter -
Juraj Majzlan -
Ling Fei Zhang -
marco antoni alsina corvalan -
Matt Newville -
scalvin＠slc.edu -
Scott Calvin -
Tsu-Chien Weng -
Van Vu