[Ifeffit] Ifeffit Digest, Vol 153, Issue 14

Marcelo Eduardo Alves mealves at gmail.com
Mon Nov 9 14:26:54 CST 2015


Thanks a lot Robert!
Marcelo.

2015-11-09 17:30 GMT-02:00 <ifeffit-request at millenia.cars.aps.anl.gov>:

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> 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 at gmail.com>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 12
> Message-ID:
>         <
> CAAO6x+ZSKvPtdLYw1nvz-iPZec1+Hcin-my0mtJDKd27_8PRnw at 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 at millenia.cars.aps.anl.gov>:
>
> > Send Ifeffit mailing list submissions to
> >         ifeffit at 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 at millenia.cars.aps.anl.gov
> >
> > You can reach the person managing the list at
> >         ifeffit-owner at 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 at usp.br>
> > To: <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
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20151109/9e8d49f2/attachment-0001.htm
> > >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 9 Nov 2015 10:05:45 -0800
> > From: Robert Gordon <ragordon at alumni.sfu.ca>
> > To: 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>
> > 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
> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
> >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20151109/1aa31f90/attachment-0001.htm
> > >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Mon, 9 Nov 2015 12:13:53 -0600
> > From: "Guanghui Zhang" <brighton30 at 126.com>
> > To: "XAFS Analysis using Ifeffit"<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>
> > 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>
> > ?????2015-11-09 12:05
> > ???Re: [Ifeffit] Opening "older" data files in the latest Athena version
> > ????"ifeffit"<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
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20151109/ccaaf6eb/attachment-0001.htm
> > >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Mon, 09 Nov 2015 13:24:07 -0500
> > From: Carolyn Carr <ccarr at chem.umass.edu>
> > To: 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>
> > 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
> >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > Ifeffit mailing list
> > 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
> >
> >
> > End of Ifeffit Digest, Vol 153, Issue 12
> > ****************************************
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20151109/74dac49c/attachment-0001.htm
> >
>
> ------------------------------
>
> Message: 2
> Date: Mon, 9 Nov 2015 11:29:48 -0800
> From: Robert Gordon <ragordon at alumni.sfu.ca>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 12
> Message-ID: <5640F42C.8030305 at alumni.sfu.ca>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> Ah, yes...special characters...??...Athena does not seem to like those
> in file names
> If I replace with Calibra??o 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 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 at millenia.cars.aps.anl.gov
> > <mailto:ifeffit-request at millenia.cars.aps.anl.gov>>:
> >
> >     Send Ifeffit mailing list submissions to
> >     ifeffit at millenia.cars.aps.anl.gov
> >     <mailto:ifeffit at 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 at millenia.cars.aps.anl.gov
> >     <mailto:ifeffit-request at millenia.cars.aps.anl.gov>
> >
> >     You can reach the person managing the list at
> >     ifeffit-owner at millenia.cars.aps.anl.gov
> >     <mailto:ifeffit-owner at 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 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>
> >     -------------- next part --------------
> >     An HTML attachment was scrubbed...
> >     URL:
> >     <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20151109/9e8d49f2/attachment-0001.htm
> >
> >
> >     ------------------------------
> >
> >     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
> >
> >     -------------- next part --------------
> >     An HTML attachment was scrubbed...
> >     URL:
> >     <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20151109/1aa31f90/attachment-0001.htm
> >
> >
> >     ------------------------------
> >
> >     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>
> >     http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >     Unsubscribe:
> http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
> >     -------------- next part --------------
> >     An HTML attachment was scrubbed...
> >     URL:
> >     <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20151109/ccaaf6eb/attachment-0001.htm
> >
> >
> >     ------------------------------
> >
> >     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
> >
> >
> >
> >     ------------------------------
> >
> >     _______________________________________________
> >     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
> >
> >
> >     End of Ifeffit Digest, Vol 153, Issue 12
> >     ****************************************
> >
> >
> >
> >
> > _______________________________________________
> > Ifeffit mailing list
> > 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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>
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