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

Demeter under El Capitan
by Fowler, Joseph W. 13 Nov '15

13 Nov '15

Bruce, Scott, Manuel: I’m the MacPorts maintainer for demeter and ifeffit, but I’m afraid I have not been much help lately. I’m sorry that I have not chimed in about any of the recent reports Mac / Macports problems under El Capitan. It so happens that my employer (US National Institute of Standards and Technology) does not let us upgrade to Yosemite OR El Capitan. They own the only Macs to which I have access, so I can only work under Mavericks. I’m afraid that artemis, hephaestus, and athena all start properly for me. To Manuel from Grenoble, all I can say is that xorg-server has a lot of dependencies, and it will take a long time to install the needed ports the first time. I would not think an entire hour is out of the question, depending on your connection speed and computer performance. To the others having trouble running (as opposed to installing), I wonder if anyone in the community is having success with the demeter suite under El Capitan? If so, we’d all be grateful if you could let us know what tricks were required. I am totally helpless on OS 10.10 and 10.11-specific problems. Joe Fowler NIST Boulder Laboratories

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Apparent bugs in Athena 0.9.24 running under Windows 7 64 bit
by Marcelo Eduardo Alves 13 Nov '15

13 Nov '15

I have run another example file (Au+Cyanobacteria) downloaded from https://github.com/bruceravel/XAS-Education in Athena 0.9.24 under Windows 7 64 bit using two different Dell computers and observed the following apparent bugs: In both computers the orange points that indicates the E0 and the limits of pre and post-edge fittings did not appear in the plots; In both computers the legends did not appear in all plots; the same for the axes's scales and titles. The LCF plot showed just the sample and the fitted normalized ones even when the standard ones were required; In one computer, there were just two choice options for the standards; in the other one these boxes worked normally and all standards could be considered. Some screenshots are attached to this message, Marcelo.

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Apparent bugs in Athena 0.9.24 under windows 7 64 bits - corrigendum
by Marcelo Eduardo Alves 13 Nov '15

13 Nov '15

Previous message: The LCF plot showed just the sample and the fitted normalized ones even when the standard ones were required Corrigendum: In fact, this is working in both computers, i.e., all plots appear in the graph; however, in one machine the legend, the axes´s scales, and the axes´s titles are not diplayed. M.

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Re: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples
by Carolyn Carr 12 Nov '15

12 Nov '15

Hi Bruce, Thanks so much for clarifying that for me! I have been basing my fitting in R-space off of XAFS spectroscopy; fundamental principles and data analysis DOI 10.1023/A:1019105310221 which has a section on fitting in R-space over k-space although it is very possible I misinterpreted its analysis. My zinc question is more of a query rather than a true problem, and so I am glad that you have taken time to correct my knowledge of how fitting works. Carolyn Carr

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LCF, Sayers & Bunker, R and ATHENA
by Florian Werner 12 Nov '15

12 Nov '15

Dear mailing list, we recently published a paper where we broke with the "Sayers & Bunker 1988 - Paradigm" to apply normalization as consistently as possible between samples and standards when performing linear combination fitting: http://pubs.acs.org/doi/abs/10.1021/acs.est.5b03096. There, we showed that for known mixtures of phosphorus standards the LCF of P K-edge XANES spectra delivers better results when changing the base-line and normalization parameters of the sample (in defined ranges, using the software /R/). I'm writing to the mailing list of several reasons: 1) A reviewer explicitly asked to contact Bruce Ravel so that the new insight could be implemented in ATHENA, 2) I was trying to combine my code with ATHENAs way of LCF before publishing the code. Unfortunately, I have not been able to resolve that a combination of both approaches results in large numbers of LCF procedures (sometimes Million or Billion). So many procedures are not fittable in reasonable time, maybe because my code is slow or maybe because /R/ isn't fast enough (or just the nlsLM-function that I'm using for LCF). I'm stuck and maybe programming in Perl would be a better choice (never programmed in Perl, yet)? Maybe a different kind of fitting algorithm would be faster?, 3) When using the nlsLM-function to perform LCF in /R/, I also have to provide portions of the standards before starting the fit. I used the same approach as ATHENA, dividing 1 by the number of standards so that every standard has the same portion. However, when playing with the code I realized that changing the starting portion can have an impact on the fitting result. Has this been observed or tested before by anyone else? How do you, in general, justify using the same starting portion for every standard? 4) Some minor question about LCF in ATHENA: a) Could the standards (the columns) in the output .csv-file after LCF be sorted alphabetically?, b) Does LCF in ATHENA sometimes produce negative numbers of a portion because the weight of any "last" standard in a set is always calculated by "1-sum(portions_of_other_standards)" (could it be this? https://github.com/bruceravel/demeter/blob/master/lib/Demeter/LCF.pm#L375-L…) To mimic "all samples sum to one" from ATHENA and to not produce negative portions, we used all LCF results which have a residual "absolute(1-sum(portions_of_all_standards)) < 0.0005"; maybe this is of interest also for ATHENA? Cheers, Florian

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Problems with EXAFS Fitting of Metalloprotein Zinc Samples
by Carolyn Carr 11 Nov '15

11 Nov '15

Hi, I have a general question rather than specific. I have only ever fit XAS data on metalloproteins and one feature that I see is that when fitting Zinc samples in R-space there is no local minima. For Cobalt and Nickel samples I typically get one or a few fits that are obviously significantly better in R-factor (with reasonable distances, sigma^2, etc) but for Zinc this is not the case. I can get many good fits and Zinc likes to increase the coordination up to 8 for all data sets I have ever fit, although there is obviously no physical basis in this. This is true of not just my own proteins but Zinc samples made by collaborators, and after looking through previous group members fit tables, they had similar issues. My understanding is that one of the benefits of fitting in R-space is that there is a local minima, whereas in k-space there are many minima. I was wondering if there was a physical basis for this feature in Zinc samples, or if perhaps my group is not aware of some experimental setup that we should be doing for Zinc that would resolve this problem. Thank you for any help regarding this matter, Carolyn Carr

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Problems with EXAFS Fitting of Metalloprotein Zinc Samples
by Carolyn Carr 10 Nov '15

10 Nov '15

Hi Robert, Thanks for your reply. We have done this with standard samples and we see the same thing. And of course, we can tell qualitatively from the XANES that our sample is not 8 coordinate, and not even 6 coordinate. We have never tried changing the temperature but we can try this the next time we go to SSRL. We actually do fit multiple scattering features as imidazoles which is one of the things we consider as a strength of Artemis for our basic needs. This is part of why we think this is strange, because putting 8 imidazoles around a zinc seems kind of silly but it likes it. 5 imidazoles and 3 sulfurs and I have an R-factor of 0.2% every time. If there is non standard multiple scattering that occurs in multiple unrelated proteins from different organisms then we would have no idea what this could be. Thanks for your comments! Carolyn Carr

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 12
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

I have downloaded the zip-file containing the example files and extracted them into other subfolders (i.e. C:\Users\Marcelo\Documents\1.Athena Calibração e Alinhamento\Examples\Fe foil). I think that this was my error. When I use C:\Fe foil the file was opened in Athena without any issue. Thank you Robert and Guanghui 2015-11-09 16:24 GMT-02:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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. Opening "older" data files in the latest Athena version > (Marcelo Eduardo Alves) > 2. Re: Opening "older" data files in the latest Athena version > (Robert Gordon) > 3. Re: Opening "older" data files in the latest Athena version > (Guanghui Zhang) > 4. Problems with EXAFS Fitting of Metalloprotein Zinc Samples > (Carolyn Carr) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Nov 2015 15:41:33 -0200 > From: "Marcelo Eduardo Alves" <mealves.esalq(a)usp.br> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Opening "older" data files in the latest Athena > version > Message-ID: <97FB7D67CF2142A48FA29F9776D0A164@MarceloPC> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I am using the latest version of Demeter (0.9.24) and I have downloaded > the data files available at https://github.com/bruceravel/XAS-Education. > > However, I am not being able to open the example files in Athena (e.g., > Fe.060 of Fe foil folder). > > Please, would it be possible to open those example files in the latest > Athena version. > > Thank you. > > Marcelo. > > > _______________________________________ > Marcelo Eduardo Alves > Departamento de Ci?ncias Exatas - ESALQ/USP > Avenida P?dua Dias, 11 > 13418-900 Piracicaba-SP > Fone: 19-3429-4151- RAMAL 26 > Email: mealves.esalq(a)usp.br >

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 14
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

Thanks a lot Robert! Marcelo. 2015-11-09 17:30 GMT-02:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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: Ifeffit Digest, Vol 153, Issue 12 (Marcelo Eduardo Alves) > 2. Re: Ifeffit Digest, Vol 153, Issue 12 (Robert Gordon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Nov 2015 17:01:51 -0200 > From: Marcelo Eduardo Alves <mealves(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 12 > Message-ID: > < > CAAO6x+ZSKvPtdLYw1nvz-iPZec1+Hcin-my0mtJDKd27_8PRnw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > I have downloaded the zip-file containing the example files and extracted > them into other subfolders (i.e. C:\Users\Marcelo\Documents\1.Athena > Calibra??o e Alinhamento\Examples\Fe foil). > I think that this was my error. > When I use C:\Fe foil the file was opened in Athena without any issue. > Thank you Robert and Guanghui > > 2015-11-09 16:24 GMT-02:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > > > 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. Opening "older" data files in the latest Athena version > > (Marcelo Eduardo Alves) > > 2. Re: Opening "older" data files in the latest Athena version > > (Robert Gordon) > > 3. Re: Opening "older" data files in the latest Athena version > > (Guanghui Zhang) > > 4. Problems with EXAFS Fitting of Metalloprotein Zinc Samples > > (Carolyn Carr) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 9 Nov 2015 15:41:33 -0200 > > From: "Marcelo Eduardo Alves" <mealves.esalq(a)usp.br> > > To: <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] Opening "older" data files in the latest Athena > > version > > Message-ID: <97FB7D67CF2142A48FA29F9776D0A164@MarceloPC> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear all, > > > > I am using the latest version of Demeter (0.9.24) and I have downloaded > > the data files available at https://github.com/bruceravel/XAS-Education. > > > > However, I am not being able to open the example files in Athena (e.g., > > Fe.060 of Fe foil folder). > > > > Please, would it be possible to open those example files in the latest > > Athena version. > > > > Thank you. > > > > Marcelo. > > > > > > _______________________________________ > > Marcelo Eduardo Alves > > Departamento de Ci?ncias Exatas - ESALQ/USP > > Avenida P?dua Dias, 11 > > 13418-900 Piracicaba-SP > > Fone: 19-3429-4151- RAMAL 26 > > Email: mealves.esalq(a)usp.br > >

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 11
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

I have downloaded the zip-file containing the example files and extracted them into other subfolders (i.e. C:\Users\Marcelo\Documents\1.Athena Calibração e Alinhamento\Examples\Fe foil). When I use C:\Fe foil the file was opened in Athena without any issue. Thank you. 2015-11-09 15:55 GMT-02:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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. Demeter under El Capitan (Fowler, Joseph W.) > 2. Re: Demeter under El Capitan (Zack Gainsforth) > 3. Opening "older" data files in the latest Athena version > (Marcelo Eduardo Alves) > 4. Re: Opening "older" data files in the latest Athena version > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Nov 2015 16:20:09 +0000 > From: "Fowler, Joseph W." <joe.fowler(a)nist.gov> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Demeter under El Capitan > Message-ID: <CAAD97E1-600B-43B3-B7AE-FAE9E373DC3E(a)nist.gov> > Content-Type: text/plain; charset="windows-1252" > > Bruce, Scott, Manuel: > > I?m the MacPorts maintainer for demeter and ifeffit, but I?m afraid I have > not been much help lately. > > I?m sorry that I have not chimed in about any of the recent reports Mac / > Macports problems under El Capitan. It so happens that my employer (US > National Institute of Standards and Technology) does not let us upgrade to > Yosemite OR El Capitan. They own the only Macs to which I have access, so I > can only work under Mavericks. I?m afraid that artemis, hephaestus, and > athena all start properly for me. > > To Manuel from Grenoble, all I can say is that xorg-server has a lot of > dependencies, and it will take a long time to install the needed ports the > first time. I would not think an entire hour is out of the question, > depending on your connection speed and computer performance. > > To the others having trouble running (as opposed to installing), I wonder > if anyone in the community is having success with the demeter suite under > El Capitan? If so, we?d all be grateful if you could let us know what > tricks were required. I am totally helpless on OS 10.10 and 10.11-specific > problems. > > Joe Fowler > NIST Boulder Laboratories > > >

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