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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?

I'm open to other solution other than Pymol, e.g. VMD.

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    $\begingroup$ No idea about pymol, but can give you advise in how you can get it in VMD. Lemme know so that I can write an answer. $\endgroup$
    – Vasista
    Oct 31, 2021 at 10:45
  • $\begingroup$ @Vasista Please do. Thanks in advance. I've modified my OP to generalize. $\endgroup$ Oct 31, 2021 at 10:46
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    $\begingroup$ @Vasista if you'd like to add an answer, it looks like the OP generalized the question to VMD or other software. $\endgroup$
    – Tyberius
    Nov 19, 2021 at 2:03
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    $\begingroup$ @Vasista The OP seems keen to learn your answer about how to do it VMD. Can you answer it? :) $\endgroup$ Jan 14, 2022 at 2:05
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    $\begingroup$ @Vasista do you think you can write an answer about how to do this in VMD? $\endgroup$ Jan 31, 2023 at 21:05

1 Answer 1

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In Pymol, the polar contacts can be visualised in the following way:

  1. Enable the sequence tab by clicking on : Display -> Sequence
  2. Select both the protein and ligand in sequence tab
  3. In the right side tab, next to the object name, click the 'A' button -> find -> polar contacts -> then you will get a list of options which you can choose -> for example you can choose : to any atoms.

The sequence of steps shown in the below picture uses the following protein ligand combination:

  • Protein : Beta chain of the Human Haemoglobin (PDB ID: 2hhb)
  • Ligand: Corresponding HEM of the beta chain

enter image description here

The polar contacts will be shown as yellow lines as shown in below picture:

enter image description here

You can replicate the same steps with your protein + ligand choose the relevant type of polar contact from the list.

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