Help: Artemis closes without error message when open .cif file
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]
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
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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (3)
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Bruce Ravel -
Daniel Whittaker -
jiahui