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

[Eric Pettersen]

Hi Marek,
	Thanks for the suggestion — I guess I don’t see many metal complexes in Mol2 files so this got overlooked.  I’ve implemented it now and it will be available in the next daily build.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Mar 13, 2017, at 8:59 AM, Marek Maly <marek.maly at 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
> 
> 
> 
> 
> 
> 
> 
> -- 
> Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/<source.mol2><Chimera_MOL2.mol2><Chimera_PDB.pdb>_______________________________________________
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