Re: [PyMOL] How to show that one docking is better than another with Pymol visually

[Peter K. <pk...@se...>]

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: pet...@ru...

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 <gun...@gm...>
> *Sent:* Friday, 9 July 2021 1:30 AM
> *To:* pymol-users <pym...@li...>
> *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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