March 2009 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] [Ifeffit-devel] import the chi. file from Artemis to Athena
by Bruce Ravel 17 Mar '09

17 Mar '09

Catalin, This is not really a question for the Ifeffit-devel mailing list. I am sending my response to the normal Ifeffit mailing list -- which is the proper place for a question about using the software. On Tuesday 17 March 2009 11:29:10 am Catalin Popescu wrote: > I am trying to align the theory and the data for one of my compounds. I > have difficulties to import in Athena the chi(k)file saved in Artemis. > Whenever i saved my fit data as a chi (k) and I tried to import it in > Athena i am asked to choose the right columns. I tried all the ways to > choose the columns but it doesn't work. How are you saving the chi(k) data from Artemis? Athena expects that its data are chi(k) and NOT k-weighted chi(k). If you are saving the data from Artemis as anything other than un-k-weighted chi(K), the wrong thing will certainly happen in Athena. When importing the chi(k) data back into Athena, you will want to select the first column as k and the second column as chi(k). > Whenever I want to check what I imported I don’t see the right > chi. file so I am assuming that the file saved from Artemis is not > saved as the right file. It’s weird because I know about the > tutorials (MoO3 for example) in which you can import the theory file > into Athena and after to align it to the data. In the case of the > tutorial of Shelly Kelly (background removing procedure for MoO3) > the file containing the theory file is included in .prj file. I am > assuming that it was done directly from Feff. In my case I run the > feff.inp file from Artemis. I already looked in the FAQ Sections and > I only found how to transfer data from Athena to Artemis not the > other way around. Also I saw that Athena import output files like > chi.dat but this format is coming from Feff and is not present in > Artemis. Can you please suggest me a solution? B -- Bruce Ravel ------------------------------------ bravel(a)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/

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Getting data from athena
by abhijeet gaur 17 Mar '09

17 Mar '09

Hi , I tried the method as told by Bruce & Scott to get the data from Athena and then plot it into Excel or Origin. I got the data of chi(R) in different columns in a notepad file but when I try to copy it in Origin or Excel all the column values got copied into one column , Thus I am not getting the required plot. Please tell me how to get the data plotted in some other plotting software. Abhijeet

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Figure conversion - color to b/w
by Jenny Cai 16 Mar '09

16 Mar '09

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 <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Monday, March 16, 2009 12:34:32 PM Subject: Re: [Ifeffit] Figure conversion - color to b/w 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(a)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(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ________________________________ Now with a new friend-happy design! Try the new Yahoo! Canada Messenger __________________________________________________________________ Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your favourite sites. Download it now at http://ca.toolbar.yahoo.com.

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Re: [Ifeffit] (no subject)
by Frenkel, Anatoly 16 Mar '09

16 Mar '09

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(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)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

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Atoms input file for PdO
by bill.schwartz＠yale.edu 13 Mar '09

13 Mar '09

Greetings I'd like to get an atoms input file for PdO. Can someone point me in the right direction for either obtaining or creating one? Thanks, Bill

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XANES
by Aimee Morey 12 Mar '09

12 Mar '09

I have collected full XANES and EXAFS spectra. I have imported the full spectrum into Athena. I am now trying to analyze using XANES, but I am have trouble figuring out how to set an absolute energy, i.e. 7709 eV = 0 eV or such, and have the energy scaled negatively and positively. It is probably super simple, can anyone please help? Thank you, Aimee -- Aimee M. Morey Graduate Assistant Department of Chemistry, U-3060 University of Connecticut 55 North Eagleville Rd Storrs, CT 06269-3060 Phone # (860) 486 - 6567 Fax # (860) 486 - 2981

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(no subject)
by Michael Jacob 11 Mar '09

11 Mar '09

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

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protonated pentatitanate
by A M 11 Mar '09

11 Mar '09

Dear All I have huge problem with my spectra for protonated pentatitanate ( H2Ti5O11 *3H2O), I’ve tried to build theoretical model for this compound (penta.cif) but unfortunately I have 5 Ti atoms in my formula, so I really don’t know what Ti I should select as a core atom...I tried with 5 different options Ti1....Ti5, so I obtained 5 different models (with distances between Ti-O in first shell sometimes very short 1.59A)... I would be very grateful for any help.... Best regards Marie

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latest version of horae in Debian
by Carlo Segre 08 Mar '09

08 Mar '09

Hi All: After a long delay, I have finally managed to make Debian packages of the new-look horae (after version 069) and upload it to the Debian archive. As usual, I have backported to the current Debian stable (lenny) and to Ubuntu intrepid and jaunty. Because of significant changes, I am not supporting Debian etch or Ubuntu hardy. The old versions of horae are still avilable for those in my archive. The packages can be obtained by putting the appropriate lines on your /etc/apt/sources.list file. Instructions are at http://debian-xray.iit.edu/ Cheers, Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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Nickel theory
by maho mah 04 Mar '09

04 Mar '09

dear all, I have calculated each one for Ni l2 l3 edges and them together myself .But satellite peak is so broadened in theorical calculation.what will I do for this?? M _________________________________________________________________ Windows Live™ Groups: Create an online spot for your favorite groups to meet. http://windowslive.com/online/groups?ocid=TXT_TAGLM_WL_groups_032009

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