I have the following Pymol visual, The green molecule is receptor and red/yellow is the ligand. In the ligand I highlighted Lysine (K) residue as yellow.

enter image description here

What I want to do is to highlight and draw the electro static contact of the ligand especially with Lysine residue. Like this in Pymol:

enter image description here

How can I achieve that?


1 Answer 1


Depends whether you work with named selections which is preferable and helpful if you want to use this Pymol session for future images. In this case, use the distance command for your two selections, one being the N of the K in your ligand and the other the O of the E of your protein.

Full syntax and examples here: https://pymolwiki.org/index.php/Distance

If you need a quick solution: in the menu Wizard, click on Measurement. Then click on the two atoms where you want the dotted line to appear in between.

  • $\begingroup$ Thanks but I'd like to see the electrostatic contact - proton and electron - like shown in my OP. $\endgroup$ Oct 31, 2021 at 11:10
  • 1
    $\begingroup$ This answer is still valid, you simply click the hydrogen not the nitrogen for your distance. However, I would suggest that you do color atomic, not element C as you currently have all elements coloured in and it's well confusing... $\endgroup$ Nov 1, 2021 at 9:56

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