Dear Rajib,
Pymol reads atom labels and positions from a coordinate file. It then
determines which atoms are bonded based on distance criteria. That is used
to draw the molecule.
Pymol also has an internal library of molecules and fragments, with atoms
and bonds, which can be used to build bigger molecules.
QM methods are required to determine an optimal molecular geometry. But
that's not something Pymol does. Just read in coordinates and draw those.
Hope it helps,
Tsjerk
On Jun 1, 2017 21:27, "Susmita/Rajib" <bkpsusmi...@gmail.com> wrote:
> No, Dr. Wassenaar, Sir! People have confused me. After two years, I am
> told that:
> [Quote]PyMol does not use QM methods. It also does not "determine the
> structures of molecules" [/Quote]
> I need my illustrious peers to clarify me regarding all my queries in
> all my posts in the present thread.
>
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