Dear all,
I had to generate a 3D molecule from SMILES to xyz. But i have noticed
that, 'sometimes', if i give a SMILES input for a cyclic molecule,
('c1ccccc1' for benzene) and convert it into xyz (3d) coordinates and take
the data to visualize in Avogadro, it is not showing a cyclic molecule at
all (showing an acyclic hexatriene type of thing). I, again, want to say
the word "sometimes", because in some other times its all perfect. So i am
afraid that whether its a fault of the SMILES format or during my Openbabel
installation something went wrong.
Regards,
Arpan
Indian Association for the Cultivation of Science, Kolkata, India
On Wed, 11 Dec 2019, 12:14 pm Arpan Choudhury, <aarp...@gmail.com> wrote:
> Dear all,
> I had to generate a 3D molecule from SMILES to xyz. But i have noticed
> that, sometimes, in 3D if i give a SMILES input for a cyclic molecule,
> ('c1ccccc1' for benzene) and convert it into xyz (3d) coordinates and take
> the data to visualize in Avogadro, it is not showing a cyclic molecule at
> all. I, again, want to say the word "sometimes", because in some other
> times its all perfect. So i am afraid that whether its a fault of the
> SMILES format or during my Openbabel installation something went wrong.
>
> Regards,
> Arpan
>
> Indian Association for the Cultivation of Science, Kolkata, India
>
>
>
> On Tue, 10 Dec 2019, 9:21 pm Geoffrey Hutchison, <
> geoff.hutchi...@gmail.com> wrote:
>
>>
>> > I am using Openbabel GUI on windows. I am converting SMILES to xyz
>> format using 'generate 3D coordinates' option. Everything is looking fine
>> (viewing in gui.svg viewer in firefox) as expected.
>>
>> I'm not sure why you're generating 3D coordinates to view a 2D format
>> (SVG).
>>
>> > But when i am taking the output xyz data to view in other molecular
>> editors like GaussView or Avogadro, it is not giving the structure as
>> viewed in gui.svg
>>
>> I'm not sure what that means. The XYZ file will be a 3D molecule, not a
>> 2D depiction.
>>
>> Perhaps you can give us a concrete example of the SMILES, the SVG and the
>> XYZ file?
>>
>> Thanks very much,
>> -Geoff
>>
>> ---
>> Prof. Geoffrey Hutchison
>> Department of Chemistry
>> University of Pittsburgh
>> tel: (412) 648-0492
>> email: geo...@pitt.edu
>> twitter: @ghutchis
>> web: https://hutchison.chem.pitt.edu/
>
>
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