I would like to be proven wrong but my feeling is, without even knowing anything about this particular system, that one cannot observe Fe-Fe pair at that distance in such complex case.
However, to approach it more rigorously, the first step would be to examine the relative "importance" factors of different paths in the output of FEFF. If Fe-Fe path is well isolated in distance and importance from others (in reality, it probably is not the case) it can be done, otherwise - not.
Anatoly
________________________________
From: ifeffit-bounces@millenia.cars.aps.anl.gov
Wback in the 70s and 80s, Powers, et. al. claimed to observe a Cu-Fe distance of 3.75A, seeing it in both the Cu and Fe edges. However, a bit of Googling shows that
this result is in some doubt. I once saw a Cr-Cr distance of 6 or 7A in a Cr-bis(arene) complex at 8K. Sometimes, the contributions from the light atoms just smear out
because the distances form a near-continuous distribution way out there, leaving a heavier scatterer like Fe visible. This can be simulated if you have a big enough cluster
size. You may run into a limit on the number of paths, though, since there will be a huge number of them. I would guess that you would only see the Fe-Fe at low temps.
I suspect that with something as floppy and as asymmetric as a protein, the MS paths won't contribute because you won't get a huge number of them piling up at one distance,
nor will you get focusing except for some nearby ligands such as carbonyls (Fe-C-O). When you do the simulation, don't forget to add in some reasonable MSRD.
mam
----- Original Message -----
From: Frenkel, Anatoly
To: ifeffit@millenia.cars.aps.anl.gov
Sent: Wednesday, March 11, 2009 4:49 PM
Subject: Re: [Ifeffit] (no subject)
I would like to be proven wrong but my feeling is, without even knowing anything about this particular system, that one cannot observe Fe-Fe pair at that distance in such complex case.
However, to approach it more rigorously, the first step would be to examine the relative "importance" factors of different paths in the output of FEFF. If Fe-Fe path is well isolated in distance and importance from others (in reality, it probably is not the case) it can be done, otherwise - not.
Anatoly
------------------------------------------------------------------------------
From: ifeffit-bounces@millenia.cars.aps.anl.gov
Hi MJacob, One note that might help--it is not strictly necessary to fit the nearest-neighbors in order to fit the iron-iron path. In a system like this, I would think you might get lucky and have a big contribution from near-neighbors, then a bunch of smeared out stuff (as Matthew Marcus suggested) that effectively cancels, and then a little iron- iron peak because the iron is a much better scatterer than all the organics. If that's what the Fourier transform looks like, then you can fit from say 4 to 5 angstroms and just use an iron path. It sounds weird, but I've done things like that once or twice with decent results. There are certainly pitfalls; for instance I might be a little nervous about some focused MS path that happens to line up with the Fe-Fe distorting the results, but it's worth a shot. --Scott Calvin Sarah Lawrence College Could you perhaps post an image of the Fourier transform of your data to the list? That would help give a sense of what might work and what wouldn't work. On Mar 11, 2009, at 5:49 PM, Frenkel, Anatoly wrote:
I would like to be proven wrong but my feeling is, without even knowing anything about this particular system, that one cannot observe Fe-Fe pair at that distance in such complex case. However, to approach it more rigorously, the first step would be to examine the relative "importance" factors of different paths in the output of FEFF. If Fe-Fe path is well isolated in distance and importance from others (in reality, it probably is not the case) it can be done, otherwise - not.
Anatoly
From: ifeffit-bounces@millenia.cars.aps.anl.gov
To: ifeffit@millenia.cars.aps.anl.gov
Sent: Wed Mar 11 09:40:31 2009 Subject: [Ifeffit] (no subject)
Hi all,
I measured Fe(II) edge EXAFS data for my protein that has two iron sites (Fe-Fe distance ~5A). My question is how to fit the model with the data? Can I discard the contribution of multiple scattering effects to the fitting? One most important information that I want to obtain is on the Fe-Fe distance. Is it enough to conclude from the raw data FT that the Fe-Fe distance in my protein sample has been changed in comparison to the Fe-Fe distance in the model (created with Feff using the crystal structure coordinates)? I try fitting using arthemis but got bad and weird results. is there any manual or step-by step guide that I can learn how to fit model of two metal sites to my data?
Anther question that I have how can I get to the past discussions in the forum- is there any database for questions and answers that I can learn on the analysis of EXAFS data?
Any help will be appreciated,
MJacob
ars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi everyone, I submitted a manuscript where XANES least-squares peak fitting was used. A figure (attached with this email) was copied from Athena. The problem is that the reviewer asked me to change the color peaks to black and white with diferent types of lines. I was trying to figure it out by myself, but failed. Could anyone help me out? Thank you in advance! Jenny __________________________________________________________________ Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your favourite sites. Download it now at http://ca.toolbar.yahoo.com.
Hi Jenny, It's strongly recommended that you export the data and use some other graphing program to produce publication-quality graphs. Athena is designed to help see your data, not to produce final graphics. --Scott Calvin Sarah Lawrence College On Mar 16, 2009, at 12:21 PM, Jenny Cai wrote:
Hi everyone,
I submitted a manuscript where XANES least-squares peak fitting was used. A figure (attached with this email) was copied from Athena. The problem is that the reviewer asked me to change the color peaks to black and white with diferent types of lines. I was trying to figure it out by myself, but failed. Could anyone help me out? Thank you in advance!
Jenny
On Monday 16 March 2009 12:21:14 pm Jenny Cai wrote:
I submitted a manuscript where XANES least-squares peak fitting was used. A figure (attached with this email) was copied from Athena. The problem is that the reviewer asked me to change the color peaks to black and white with diferent types of lines. I was trying to figure it out by myself, but failed. Could anyone help me out? Thank you in advance!
Jenny, The figures from Ifeffit and friends are not really intended to be of sufficient quality for a publication. See questions 10 and 11 at http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions You may find Richard Mayes' suggestion in the answer to question 10 helpful. Athena gives you quite enough information to replicate your plot in other plotting software. The line shapes are all standard line shapes and the parameters are reported after the fit. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Thank you, Bruce and Scott. Actually, I replotted all my figures using EXCEL except this one. It worked well for individual spectrum and linear combination fitting, but in least-squares peak fitting, I couldn't find the data for Gaussian and arctangent step peaks. Could you please let me know where I can find those data? Thanks again.
Jenny
________________________________
From: Bruce Ravel
I submitted a manuscript where XANES least-squares peak fitting was used. A figure (attached with this email) was copied from Athena. The problem is that the reviewer asked me to change the color peaks to black and white with diferent types of lines. I was trying to figure it out by myself, but failed. Could anyone help me out? Thank you in advance!
Jenny, The figures from Ifeffit and friends are not really intended to be of sufficient quality for a publication. See questions 10 and 11 at http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions You may find Richard Mayes' suggestion in the answer to question 10 helpful. Athena gives you quite enough information to replicate your plot in other plotting software. The line shapes are all standard line shapes and the parameters are reported after the fit. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel 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 __________________________________________________________________ Get the name you've always wanted @ymail.com or @rocketmail.com! Go to http://ca.promos.yahoo.com/jacko/
participants (5)
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Bruce Ravel
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Frenkel, Anatoly
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Jenny Cai
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Matthew Marcus
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Scott Calvin