On Mar 13, 2017, at 8:59 AM, Marek Maly <marek.maly@ujep.cz> wrote:

Hello,

it seems that Chimera (1.11.2) has problem to save some bonds in MOL2 format.

If you open attached file "source.mol2" , Chimera reads/show perfectly all
the bonds including those where is "Ru" atom present, but when you save it in MOL2
format in Chimera (see attached file "Chimera_MOL2.mol2"), then all the "Ru-x" bonds are omitted
and naturally if you open this "Chimera MOL2" file in Chimera no "Ru-x" bonds are shown.

Interestingly, if the original MOL2 file "source.mol2" is opened in Chimera and then saved
in PDB format ("Chimera_PDB.pdb"), all bonds are written and so if this PDB file is opened
in Chimera all bonds are visualized.

Would be nice if the perfect bond preservation which works in MOL2->PDB case worked also
in MOL2->MOL2 case.

  Best wishes,

      Marek







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