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#492 12-coordinate bonds not displayed

open
nobody
Open Babel (66)
3
2012-09-12
2010-10-06
Anonymous
No

There seems to be a limit on the number of bonds a particular atom may have. I am working with transition metals which may be bonded to 12 other atoms. These bonds should be displayed. I am attaching a set of xyz coordinates for a Pt13 cluster which demonstrate this problem along with images produced (incorrectly) with Avogadro and (correctly) with Jmol.

I am using Avogadro 1.0.1 on Mac OS X 10.6.4.

Discussion

  • Nobody/Anonymous

    Nobody/Anonymous - 2010-10-06

    Coordinates and images demonstrating missing bond problem

     
    pt13.zip

  • Konstantin Tokarev

    Konstantin Tokarev - 2010-10-06

    One may argue if it's correct to treat these interactions as "bonds"...

     

  • Geoff Hutchison

    Geoff Hutchison - 2011-01-23

    There is a maximum number of bonds interpreted by Open Babel into an XYZ file. It can certainly be raised, but I don't think I'd consider 12-coordinate as a likely TM state. Actinides maybe?