[Chimera-users] possible Chimera bug - saving bonds in MOL2 format

Marek Maly marek.maly at ujep.cz
Mon Mar 13 08:59:09 PDT 2017


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







-- 
Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
http://www.opera.com/mail/
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