Hello,
Try calculating the solvent accessible surface areas of the docked and
undocked molecules, including the ligand. Color atoms whose water
accessible surfaces are reduced or eliminated by the docking differently
from the rest of the structures. As an added feature, you might color
occluded hydrophobic surfaces differently from occluded hydrophilic
surfaces, but if you do that, use atom hydrophobicity and hydrophilicity
and not whole amino acid; lysine has four hydrophobic methylene groups
and one polar group. All atoms of peptides are polar, etc.
With good wishes,
Peter
--
Peter C. Kahn, Ph.D.
Professor of Biochemistry
Department of Biochemistry & Microbiology
Rutgers University
76 Lipman Drive
New Brunswick, NJ 08901
Telephone: 848-932-5618
Telefax: 732-932-8965
Email: peter.k...@rutgers.edu
On 7/19/2021 5:16 PM, Joel Tyndall wrote:
This is an intriguing question, however I don’t have an answer for you.
I would however, turn off the hydrogens as this would make the
visualisation easier on the eye. Without knowing the full context of the
figure, it is difficult to interpret further. Text can be the best way
here.
Joel
*From:*Gundala Viswanath <gunda...@gmail.com>
*Sent:* Friday, 9 July 2021 1:30 AM
*To:* pymol-users <pymol-users@lists.sourceforge.net>
*Subject:* [PyMOL] How to show that one docking is better than another
with Pymol visually
Hi
I have the following docking results.
|Dock_1|has a better energy score than|Dock_2|. What I want to do is to
show with Pymol that|Dock_1|is better visually.
Here I use a hydrogen bond, highlighted with Yellow (|Dock_1|) and Gray
(|Dock_2|). But as you can see, with that I can't show that|Dock_1|is
clearly better. That's why I'm looking for a better alternative than
hydrogen bonds.
G.V.
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