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Today's Topics:
1. Help: Artemis closes without error message when open .cif
file (jiahui)
2. Re: Help: Artemis closes without error message when open .cif
file (Bruce Ravel)
3. Re: Help: Artemis closes without error message when open.cif
file (Daniel Whittaker)
----------------------------------------------------------------------
Message: 1
Date: Mon, 10 Dec 2012 15:42:27 -0000
From: "jiahui" <qijiahui.uk@gmail.com>
To: <ifeffit@millenia.cars.aps.anl.gov>
Subject: [Ifeffit] Help: Artemis closes without error message when
open .cif file
Message-ID: <50c602e5.424cb40a.0dd5.42e3@mx.google.com>
Content-Type: text/plain; charset="us-ascii"
Dear list,
I am having this problem when I try to open the crystal structure file in
.cif format. I've tried many times already--each time when I try to open the
crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will
close by themselves without any error message.
What can I do to solve this problem and carry on with my work? I am using
Demeter 0.9.13 version.
Thank you very much for your help,
[jiahui]
------------------------------
Message: 2
Date: Mon, 10 Dec 2012 10:48:21 -0500
From: Bruce Ravel <bravel@bnl.gov>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Help: Artemis closes without error message when
open .cif file
Message-ID: <61620056.C2dlAnbQpv@lachesis.bnl.gov>
Content-Type: text/plain; charset="us-ascii"
Jiahui,
It would be helpful to me to see an example of a CIF file that
triggers this problem. If you are running on Windows, then I would
also like to see the contents of the %APPDATA%\demeter\dartemis.log
file. See
http://bruceravel.github.com/demeter/pods/bugs.pod.html
If you are a linux user, I would need to see the messages sent to the
terminal, which requires running the program from the terminal rather
from some launcher widget.
As I have said many times before on this mailing list, CIF support is
rather weak at this time. I am using a CIF parsing tool written by
someone else and it has its problems. That said, as people report
these problems, I am able to build more smarts into Demeter so that it
at least deals gracefully with a CIF file it doesn't understand.
Cheers,
B
On Monday, December 10, 2012 03:42:27 PM jiahui wrote:
> Dear list,
>
> I am having this problem when I try to open the crystal structure file in
> .cif format. I've tried many times already--each time when I try to open the
> crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will
> close by themselves without any error message.
> What can I do to solve this problem and carry on with my work? I am using
> Demeter 0.9.13 version.
>
> Thank you very much for your help,
>
> [jiahui]
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
Homepage: http://xafs.org/BruceRavel
Software: https://github.com/bruceravel
------------------------------
Message: 3
Date: Mon, 10 Dec 2012 16:16:00 -0000
From: "Daniel Whittaker" <daniel.whittaker@postgrad.manchester.ac.uk>
To: "XAFS Analysis using Ifeffit" <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Help: Artemis closes without error message when
open.cif file
Message-ID: <6229BE20E02F4353A75ACA302F4B84CD@mbdx5dw2PC>
Content-Type: text/plain; format=flowed; charset="iso-8859-1";
reply-type=original
Hi Jiahui,
I have experienced similar issues with cif files - there are so many
slightly different formats.
I found a solution was to open the file in Mercury:
http://www.ccdc.cam.ac.uk/free_services/mercury/downloads/
Save it as a .cif from within the program itself and then read it into
(D)Artemis. If that works then brilliant :) - If not then there are a few
other issues I have found working on my organic systems:
1) If there is any disorder I find it best to remove it.
2) When running atoms I have found it can produce an error. In this case, if
you save the file it produces (*.inp) then open this in a text editor and
remove any duplicate atoms (normally near the bottom of the file) save it
again and then reopen in Atoms then it should work fine.
I hope this helps troubleshoot your issues for now?
Regards,
Dan
Daniel Whittaker, MChem
Nuclear FiRST DTC PhD Student
Chemistry Building
The University of Manchester
Brunswick Street
Manchester
M13 9PL
-----Original Message-----
From: Bruce Ravel
Sent: Monday, December 10, 2012 3:48 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Help: Artemis closes without error message when
open.cif file
Jiahui,
It would be helpful to me to see an example of a CIF file that
triggers this problem. If you are running on Windows, then I would
also like to see the contents of the %APPDATA%\demeter\dartemis.log
file. See
http://bruceravel.github.com/demeter/pods/bugs.pod.html
If you are a linux user, I would need to see the messages sent to the
terminal, which requires running the program from the terminal rather
from some launcher widget.
As I have said many times before on this mailing list, CIF support is
rather weak at this time. I am using a CIF parsing tool written by
someone else and it has its problems. That said, as people report
these problems, I am able to build more smarts into Demeter so that it
at least deals gracefully with a CIF file it doesn't understand.
Cheers,
B
On Monday, December 10, 2012 03:42:27 PM jiahui wrote:
> Dear list,
>
> I am having this problem when I try to open the crystal structure file in
> .cif format. I've tried many times already--each time when I try to open
> the
> crystal structure file in *.cif format, both (D)Atoms and (D)Artemis will
> close by themselves without any error message.
> What can I do to solve this problem and carry on with my work? I am using
> Demeter 0.9.13 version.
>
> Thank you very much for your help,
>
> [jiahui]
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
Homepage: http://xafs.org/BruceRavel
Software: https://github.com/bruceravel
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