The default conformer generator in RDKit is plain distance geometry, which is
known to not be able to provide perfectly flat aromatic rings.
You can use the ETKDG conformer generator instead:
AllChem.EmbedMolecule(mol, params=AllChem.ETKDGv2())
Best,
Sereina
> On 6 Jul 2018, at 17:54, Phuong Chau <[email protected]> wrote:
>
> Follow up question regarding to PDB file:
>
> Thank you for your help. I was able to create the non-zero coordinates of the
> chemical. However, when I tried to view it on VMD, the chemical that I used
> is c1ccccc1 (benzene). The ring itself (and the atoms coming off it, which
> are mostly hydrogens) should all be in-plane but the pdb file shows that it
> is slightly puckered. Would anyone explain this for me? How can I make it be
> in-plane ?
>
> Here is a screenshot of the molecule.
> <Screenshot from 2018-07-06 09-53-12.png>
>
>
> On Fri, Jul 6, 2018 at 6:21 AM, Dmitri Maziuk via Rdkit-discuss
> <[email protected]
> <mailto:[email protected]>> wrote:
> On 7/5/2018 1:39 PM, Paolo Tosco wrote:
>
> As the PDB format includes no stereochemistry, no coordinates are needed, and
> by default they are zero, as the molecule does not have a conformation yet.
>
> Hmm. One could argue that PDB format *is* 3D coordinates, so a block with all
> zeroes is quite pointless. And of course counter-intuitive.
>
> Dima
>
>
>
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>
> --
> Phuong Chau
> Smith College '20
> Engineering Major
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