Hi Bruce, I am a windows user. The two log file(Artemis and Atoms) and one of the CIF files I used are attached to this email. Please let me know if you need more information, Hi Dan, I use Mercury to open the CIF file then save as another CIF file as you suggested. The new CIF file can be read by (D)Artemis with an warning message basically says there're some problem with this file and some possible ways to solve the problem(s). I actually went to download an old version of IFEFFIT: Ifeffit 1.2.11. This version can read the CIF files. I ran atoms and FIFF on it. Then save the file. It could be opened by (D)Artemis without problem. Thank you very much for your help and solutions, Jiahui -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: 10 December 2012 18:00 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 118, Issue 6 Send Ifeffit mailing list submissions to ifeffit@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@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner@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. 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" To: 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 To: XAFS Analysis using Ifeffit 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]

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-- 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" To: "XAFS Analysis using Ifeffit" 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]

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-- 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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 118, Issue 6 ***************************************