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#377 Wrong geometries

v_0.9.0
closed
Marcus D. Hanwell
Open Babel (66)
5
2012-09-12
2009-08-04
Anonymous
No

When opening output files like .log from GAMESS or .out from Gaussian, Avogadro imports the geometries, but wastes them. In particular, the angels are wrong, bonds are missing and the carbon atoms mostly are "flat".

I don't know, when the problem occurred the first time, but I remember it working. Probably since 0.9.4 or so...

Operating System: Gentoo / 2.6.30 / KDE 4.2.4
Avogadro Version: 0.9.7 (Portage Tree)
OpenBabel Version: 2.2.0
Language: German

Discussion

  • Michael Banck

    Michael Banck - 2009-08-04

    Can you please attach one (or more) of the files which are not read in correctly?

    Thanks.

     

  • Nobody/Anonymous

    Nobody/Anonymous - 2009-08-04

    Ok, after reinvestigating the problem ist turned out, that this is only a bug concerning opening files from within avogadro through the "open with" option. Opening the files from a menu or like "avogadro $i" works perfectly. Thats weird.

    I attched two files. One GAMESS and one Gaussian output which shows this behavior. But I can see it on every file I use.

    Thanks.

     

  • Wilhelm Eger

    Wilhelm Eger - 2009-08-04

    I don't see a button or similar for uploading files even after creating an account. Can you point me to the right option? Thanks!

     

  • Geoff Hutchison

    Geoff Hutchison - 2009-08-05

    Down at the bottom of this page, there's a section which says "Attach a file" and "Add a file." Click there and you can upload a file.

    Thanks!

     

  • Wilhelm Eger

    Wilhelm Eger - 2009-08-05

    There are only the sections "Attached File" and "Change" where I can expand boxes which say "No Files Currently Attached". No "add a file" like "add a comment". Maybe that's because this bug was opened by anonmyous? should I reopen it as a user?

     

  • Michael Banck

    Michael Banck - 2009-08-06

    Hrm, indeed it looks like the bug tracker got less useful recently, I seem to remember it was possible in the past. So unless Geoff (or one of the other admins) is able to reassign you as submitter, reporting a new bug and attaching it there might be the best option.

     

  • Marcus D. Hanwell

    Marcus D. Hanwell - 2009-08-22

    I still see add files. Can you add a file now? May be they disabled it temporarily? It would be good to get to the bottom of this issue, I have not hit this in my testing.

     

  • Marcus D. Hanwell

    Marcus D. Hanwell - 2009-08-24

    Wilhelm reported via a private message that this bug is no longer present, and so I am closing this report.