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

Error when first opening Athena on Mac
by Laura E Wasylenki 05 Mar '19

05 Mar '19

Hello, I’ve just attempted to install Demeter on a Mac running OS 10.13.6 (High Sierra). When I open Athena, the XAS processing window appears, but then a warning window appears on top of it that says “Demeter::Templates::D” used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm. I think a line number follows, but it is cut off. The warning contains several more lines that are identical to that one, except that D is replaced by other letters. When I dismiss the warning window by clicking “OK,” Athena and Perl just close down. Has anyone seen this, and does anyone know the solution? Thank you! —Laura ____________________________ Dr. Laura Wasylenki Associate Professor School of Earth and Sustainability Department of Chemistry & Biochemistry Northern Arizona University PO Box 5698, 700 S Osborne Drive Flagstaff, AZ 86011 laura.wasylenki(a)nau.edu<mailto:laura.wasylenki@nau.edu>

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Re: [Ifeffit] Ifeffit Digest, Vol 193, Issue 4
by Christopher Chantler 03 Mar '19

03 Mar '19

PS Simon, we are just around the corner [physics] and also link up with the Dementia work, so you might just drop across and have a chat / meeting! -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Monday, 4 March 2019 10:06:37 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 193, Issue 4 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Cu K edge XANES stds (Simon James) ---------------------------------------------------------------------- Message: 1 Date: Sun, 3 Mar 2019 23:06:19 +0000 From: Simon James <s.james(a)florey.edu.au> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Cu K edge XANES stds Message-ID: <A9A1ED50-AC0D-47F8-9D5D-2208001097E1(a)florey.edu.au> Content-Type: text/plain; charset="utf-8" Hi Drew, Thank you for your swift reply. Apologies for the delay in my response but I was dragged in to other matters. Appreciate the data and ref. Regarding the sanity check I have collected some spatially resolved Cu XANES ?maps? of cultured cells and some of the standards I collected during the run are horribly compromised for unclear reasons and I just wanted some clean data to reference while I work on cleaning up (to the degree possible) my standards. Thanks again. Cheers, Simon Simon James PhD Senior Research Officer NHMRC-ARC Dementia Research Development Fellow Melbourne Dementia Research Centre University of Melbourne The Florey Institute of Neuroscience and Mental Health Web: www.florey.edu.au<http://www.florey.edu.au> On 28 Feb 2019, at 2:51 am, Latta, Drew E <drew-latta(a)uiowa.edu<mailto:drew-latta@uiowa.edu>> wrote: Hi Simon, Since you are just looking for a sanity check (on what??) here are some Cu-S standards for you. They were published in DOI: 10.1021/es304736y. The Cu-cys sample is not a pure phase, but probably a mixture of cysteine/cystine. But it is likely mostly Cu(I). Further discussion is available in the SI of the paper above. The file is from an old, old version of Athena (0.8x)... hopefully it works for you. Best, Drew Latta ====================================== Drew E. Latta, Ph.D. Asst. Research Scientist The University of Iowa Civil and Environmental Engineering/IIHR 4105 Seamans Center Iowa City, IA 52242 Ph. 319-936-0034 email. drew-latta(a)uiowa.edu<mailto:drew-latta@uiowa.edu> ====================================== -----Original Message----- From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Simon James Sent: Tuesday, February 26, 2019 3:18 PM To: Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> Subject: [Ifeffit] Cu K edge XANES stds Hi mailing list, I am hoping someone is willing to share their Cu K-edge XANES spectra from biological Cu thiol complexes. I?m particularly interested in Cu(I/II)-GSH, Cu(I/II)-Cys or similar. I need a sanity check on some fluorescence data I am wrangling. Can anyone help? Best regards, Simon This mail was composed on the move via my phone. Apologies for any typos. Florey Institute of Neuroscience and a Mental Health Melbourne Brain Centre 30 Royal Pde Parkville, 3052 VIC _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit <Cu_Samples_athena.prj>_______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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Cu K edge XANES stds
by Simon James 03 Mar '19

03 Mar '19

Hi mailing list, I am hoping someone is willing to share their Cu K-edge XANES spectra from biological Cu thiol complexes. I’m particularly interested in Cu(I/II)-GSH, Cu(I/II)-Cys or similar. I need a sanity check on some fluorescence data I am wrangling. Can anyone help? Best regards, Simon This mail was composed on the move via my phone. Apologies for any typos. Florey Institute of Neuroscience and a Mental Health Melbourne Brain Centre 30 Royal Pde Parkville, 3052 VIC

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*****SPAM*****Creating EXAFS coefficient file for reverse monte carlo simulation
by tolga.ulucan＠metu.edu.tr 03 Mar '19

03 Mar '19

Hello everyone, I have synchrotron XRD and XAFS(L3 Tb edge) data on Al90Tb10 metallic glass alloy that i want to use them as constraints in a reverse monte carlo simulation(RMC_POT). RMC_POT manual says i need 2 files for XAFS. 1st chi(k)-k file which i exported from athena as normalized data and 2nd exafs coefficient file which i don't understand what it is or how to create it. I was wondering if anyone can help me on how to create this file or point me on a direction to get more info on this? Best wishes, Tolga Han Ulucan

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Data on Cd5H2(PO4)4·4H2O
by 1510405＠tongji.edu.cn 02 Mar '19

02 Mar '19

Hi all, I have acquired Cd L3-edge XANES spectra of my sample and some Cd standards for LCF analysis. However, I lack the spectra of Cd5H2(PO4)4·4H2O, which was important to my analysis. Therefore, I was wondering if anyone could share the Cd L3-edge XANES data of Cd5H2(PO4)4·4H2O with me? Best regards, Sicong Lei

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Can't load Iffeffit.dll
by Haas, de, W.B. 01 Mar '19

01 Mar '19

Dear mailing list, I recently started using Windows 10 Enterprise. However, now Athena, Artemis and Hephaestus don't launch (I see the the software icon but then it doesn't launch). I tried the suggestions made in an earlier thread but they didn't work for me: 1. Making sure there is permission to read and write in the location where Demeter is installed. 2. Making sure the antivirus software doesn't misidentify it as a threat. The CIT services of my university don't know how to solve this issue either. So I was wondering whether there were any other fixes known for this issue. The earlier thread: [Ifeffit] Problems Running Athena, Artemis and Hephaestus on P.C. with Windows 7 Enterprise Operating System May 2016 http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2016-May/008592.html Kind regards, Winfried de Haas

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Larch 0.9.42
by Matt Newville 26 Feb '19

26 Feb '19

Hi Folks, Larch 0.9.42 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/installation.html Version 0.9.42 fixes many problems, especially to the XAS Viewer GUI app which is now pretty close to a replacement for Athena but with better peak-fitting and with none of the limitations that were imposed by the outdated ifeffit library. For MacOSX, Version 0.9.42 can be installed with a standard Mac "pkg" installer file. If you have already installed Larch, you should be able to update to the latest version with conda update -c gsecars xraylarch on Windows, you may have to specify the full path with something like: C:\Users\<YourName>\AppData\Local\Continuum\xraylarch\Scripts\conda.exe -c gsecars xraylarch If you have any trouble upgrading, you can also simply remove the XrayLarch installation and reinstall using one the installers above. For Python programmers, Version 0.9.42 ends support for Python 2. No testing or packaging was done with Python 2 for this release, and going forward the master development branch will not work with Python 2. Please let us know if you having any questions, trouble, or suggestions. --Matt Newville

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Problem with using lincomb_fit function in the Larch
by Tayal, Akhil 26 Feb '19

26 Feb '19

Hello Matt, I could not be able to perform LCA using the lincomb_fit function in the Larch software. I am getting the error message from line number 80 in the lincombo_fitting.py script. I expect the function has some bug with reading the group values. It could not be even able to read the default array 'norm' nither any user-provided 'arrayname' such as 'flat or fpp.' Can you suggest any solution for it? Please find the data files and larch script I am using for this purpose. Thanks, Akhil

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Does anyone have XAS from Cu(I)-GSH and/or Cu(I)-cys
by Simon James 24 Feb '19

24 Feb '19

Hi mailing list, I am hoping someone can help me sanity check some XAS spectra I recorded. I have [Cu(I)cys], [Cu(I)GSH] spectra (recorded in fluorescence) and would be eternally grateful if anyone is prepared to share any of their data on these or similar compounds? I am really only interested in the edge but more data is always more data. Happy to discuss offline if preferred. Happy XAS'ing Best regards, Simon Simon James Senior Research Officer NHMRC-ARC Dementia Research Development Fellow Melbourne Dementia Research Centre University of Melbourne The Florey Institute of Neuroscience and Mental Health Office: +61 (3) 9035 6420 Mob: +61 (4) 3811 0982 Web: www.florey.edu.au<http://www.florey.edu.au> simon.james(a)florey.edu.au<mailto:simon.james@florey.edu.au>

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Hafnia standards
by Mukundan, Vineetha 21 Feb '19

21 Feb '19

Hi All, I am new to EXAFS data analysis and am working on Hafnia based dielectrics. So far, I have not measured reference standards of hafnia. I know my samples have monoclinic and orthorhombic phases. If anyone on this mailing list have these standards and don't mind sharing, please email me. Alternatively if there are ways to generate/simulate it (perhaps using FEFF and the corresponding .cif files), please let me know. Thank you, Vineetha

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