[Ifeffit] Ifeffit Digest, Vol 153, Issue 12
Robert Gordon
ragordon at alumni.sfu.ca
Mon Nov 9 13:29:48 CST 2015
Ah, yes...special characters...çã...Athena does not seem to like those
in file names
If I replace with Calibração with Calibracao in a test directory of my
own, then the file opens without issue.
-R.
On 11/9/2015 11:01 AM, Marcelo Eduardo Alves wrote:
> 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 at millenia.cars.aps.anl.gov
> <mailto:ifeffit-request at millenia.cars.aps.anl.gov>>:
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> 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 at usp.br
> <mailto:mealves.esalq at usp.br>>
> To: <ifeffit at millenia.cars.aps.anl.gov
> <mailto:ifeffit at millenia.cars.aps.anl.gov>>
> Subject: [Ifeffit] Opening "older" data files in the latest Athena
> version
> Message-ID: <97FB7D67CF2142A48FA29F9776D0A164 at 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 at usp.br <mailto:mealves.esalq at usp.br>
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> ------------------------------
>
> Message: 2
> Date: Mon, 9 Nov 2015 10:05:45 -0800
> From: Robert Gordon <ragordon at alumni.sfu.ca
> <mailto:ragordon at alumni.sfu.ca>>
> To: ifeffit at millenia.cars.aps.anl.gov
> <mailto:ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Opening "older" data files in the latest Athena
> version
> Message-ID: <5640E079.8010405 at alumni.sfu.ca
> <mailto:5640E079.8010405 at alumni.sfu.ca>>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> Hi Marcelo,
>
> How did you save the data file?
> I can open Fe.060 without issue using 0.9.22 but in order to do so,
> I clicked on the fe.060 link, then selected RAW and then saved as
> text.
> If I just right-clicked and saved link as from the list page, I
> ended up
> with
> some html document.
>
> regards,
> Robert
>
> On 11/9/2015 9:46 AM, Marcelo Eduardo Alves wrote:
> > I have downloaded the worked examples available at
> > https://github.com/bruceravel/XAS-Education
> >
> > However, I am not being able to open them in the latest Athena
> version
> > (0.9.24) (e.g., Fe.060 of Fe foil folder).
> >
> > Could those files be opened in the last Athena version?
> >
> > Thank you.
> >
> > Marcelo.
> >
> >
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
> <mailto:Ifeffit at 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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> ------------------------------
>
> Message: 3
> Date: Mon, 9 Nov 2015 12:13:53 -0600
> From: "Guanghui Zhang" <brighton30 at 126.com
> <mailto:brighton30 at 126.com>>
> To: "XAFS Analysis using
> Ifeffit"<ifeffit at millenia.cars.aps.anl.gov
> <mailto:ifeffit at millenia.cars.aps.anl.gov>>
> Subject: Re: [Ifeffit] Opening "older" data files in the latest Athena
> version
> Message-ID: <6b2b48e5.6.150ed73086d.Coremail.brighton30 at 126.com
> <mailto:6b2b48e5.6.150ed73086d.Coremail.brighton30 at 126.com>>
> Content-Type: text/plain; charset="utf-8"
>
> Marcelo,
> I am currently using the Demeter 0.9.24, and I can open the Fe.060
> file without any problem. As Robert mentioned, I saved the raw
> data as text file.
>
> Guanghui
>
>
> 2015-11-09
>
>
>
>
>
>
>
>
> ????Robert Gordon <ragordon at alumni.sfu.ca
> <mailto:ragordon at alumni.sfu.ca>>
> ?????2015-11-09 12:05
> ???Re: [Ifeffit] Opening "older" data files in the latest Athena
> version
> ????"ifeffit"<ifeffit at millenia.cars.aps.anl.gov
> <mailto:ifeffit at millenia.cars.aps.anl.gov>>
> ???
>
> Hi Marcelo,
>
> How did you save the data file?
> I can open Fe.060 without issue using 0.9.22 but in order to do so,
> I clicked on the fe.060 link, then selected RAW and then saved as
> text.
> If I just right-clicked and saved link as from the list page, I
> ended up with
> some html document.
>
> regards,
> Robert
>
>
> On 11/9/2015 9:46 AM, Marcelo Eduardo Alves wrote:
>
> I have downloaded the worked examples available at
> https://github.com/bruceravel/XAS-Education
>
> However, I am not being able to open them in the latest Athena
> version (0.9.24) (e.g., Fe.060 of Fe foil folder).
>
> Could those files be opened in the last Athena version?
>
>
> Thank you.
>
>
> Marcelo.
>
>
>
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> <mailto:Ifeffit at millenia.cars.aps.anl.gov>
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> ------------------------------
>
> Message: 4
> Date: Mon, 09 Nov 2015 13:24:07 -0500
> From: Carolyn Carr <ccarr at chem.umass.edu
> <mailto:ccarr at chem.umass.edu>>
> To: ifeffit at millenia.cars.aps.anl.gov
> <mailto:ifeffit at millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc
> Samples
> Message-ID: <20151109132407.99127g2zy7ipeldz at umail.oit.umass.edu
> <mailto:20151109132407.99127g2zy7ipeldz at umail.oit.umass.edu>>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> 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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>
> End of Ifeffit Digest, Vol 153, Issue 12
> ****************************************
>
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