PyMol does not use QM methods. It also does not "determine the structures of
molecules".
-David
> On Jun 1, 2017, at 12:38 AM, Susmita/Rajib wrote:
>
> Thank you, Dr. Tyugashev, for replying to my query.
> Doesn't PyMol also use those QM methods to determine the structures of
> molecules?
> Th
How come we see structures of molecules in PyMol?
https://en.wikipedia.org/wiki/PyMOL
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Hi Rajib,
The bonds are determined based on a distance cutoff.
Hope it helps,
Tsjerk
On Jun 1, 2017 21:15, "Susmita/Rajib" wrote:
How come we see structures of molecules in PyMol?
https://en.wikipedia.org/wiki/PyMOL
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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.
--
Hi Rajib,
Probably part of the confusion is due to the meaning of "determine the
structure". I understand "determine" can have different meaning in
different contexts. In my area of research "determine" generally means to
use experimental methods like X-ray crystallography or NMR to establish the
[Quote]...structural determination is performed with different
programs that have nothing...[/Quote]
Different programs?!
Could you elaborate further please, Sir!
What would be a comprehensive program for QM determination of
individual Bond Dissociation Energy for any bond (particularly,
organic)?
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
[Quote]
On 02/06/2017, Osvaldo Martin wrote:
...send me a private message if you want further details on
this topic ...[/Quote]
Sir, I wouldn't want to waste your precious time!
Not chemical reaction per se, Sir, but only Bond Dissociation Energies
of individual bonds breaking and bonds forming ..
And finally, Dr. Timofey Tyugashev, who was the first to post his
response to my query, perhaps put in a comma between "Bond" and
"Dissociation" in the subject head, "[PyMOL] Is it possible in Pymol
to determine Individual Bond, Dissociation Energy for any Bond in
organic molecules?" which changed
