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

Marek Maly marek.maly at ujep.cz
Mon Mar 13 20:16:51 PDT 2017


Thanks a lot Eric !

    Best wishes,

      Marek



Dne Tue, 14 Mar 2017 01:50:27 +0100 Eric Pettersen <pett at cgl.ucsf.edu>  
napsal/-a:

> 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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>
>
>
>
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