2015-11-09 16:24 GMT-02:00 <ifeffit-request@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)

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Message: 1
Date: Mon, 9 Nov 2015 15:41:33 -0200
From: "Marcelo Eduardo Alves" <mealves.esalq@usp.br>
To: <ifeffit@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@usp.br
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Message: 2
Date: Mon, 9 Nov 2015 10:05:45 -0800
From: Robert Gordon <ragordon@alumni.sfu.ca>
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Opening "older" data files in the latest Athena
version
Message-ID: <5640E079.8010405@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@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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Message: 3
Date: Mon, 9 Nov 2015 12:13:53 -0600
From: "Guanghui Zhang" <brighton30@126.com>
To: "XAFS Analysis using Ifeffit"<ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Opening "older" data files in the latest Athena
version
Message-ID: <6b2b48e5.6.150ed73086d.Coremail.brighton30@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@alumni.sfu.ca>
?????2015-11-09 12:05
???Re: [Ifeffit] Opening "older" data files in the latest Athena version
????"ifeffit"<ifeffit@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.

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Message: 4
Date: Mon, 09 Nov 2015 13:24:07 -0500
From: Carolyn Carr <ccarr@chem.umass.edu>
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc
Samples
Message-ID: <20151109132407.99127g2zy7ipeldz@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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