Hi Célien,
In my understanding, since every aromatic carbon is sp2 hybridized, PyMOL's
output is not wrong. The problem is that PyMOL only knows about delocalized
bonds, it doesn't have a proper concept of aromaticity (doesn't implement
Hückel's rule). For example you sometimes also see PyMOL's "aromatic" bonds on
carboxyl groups.
There is actually some code to classify atoms with delocalized bonds as
aromatic for MOL2 output, but it's disabled:
https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/Mol2Typing.cpp#l35
Bonds are exported as aromatic (ar) because the MOL2 format doesn't have a
"delocalized" type, so "ar" is still the best match for PyMOL's classification.
Hope that helps.
Cheers,
Thomas
> On Nov 14, 2017, at 12:10 PM, Célien Jacquemard - Employé
> wrote:
>
> Hello,
>
> I'm using PyMOL 1.8.6.1 (64 bits) on a Linux distribution (CentOS 7). I used
> PyMOL API for CE alignment (protein and ligand) with a reference (target)
> protein. Then, I saved the aligned protein and ligand. Input and output
> format are mol2. However, I noticed that atomic types from aromatic ring
> aren't correct. From the input file, type is 'C.ar' but becomes 'C.2' in the
> output file. The right bond type is conserved (C.ar).
>
> So my question is: Is it a bug or an expected behavior ?
>
> Best regards
>
> Célien Jacquemard
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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