text: user6199: I have the following docking results:
  Dock_1 has 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 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 better alternative than hydrogen bond.
  
  
  user12181: maybe you can use the "per-residue interaction scores" (wich is available via Schrödinger).
  On the other hand,to show if a Docking Pose is really "better" you could show specific interactions rather than the complete big molecule.. e.g. an important salt bridge is missing. (hydrogen bonds are not that important, due to the fact that they can be bridged with water molecules)
  Sorry, this is not really a solution, but I am not allowed to comment jet -.-
  
original_text: 6199: <p>I have the following docking results:</p>
  <p><code>Dock_1</code> has better energy score than <code>Dock_2</code>.
  What I want to do is to show with Pymol that <code>Dock_1</code> is better visually.</p>
  <p>Here I use hydrogen bond, highlighted with Yellow (<code>Dock_1</code>) and Gray (<code>Dock_2</code>).
  But as you can see, with that I can't show that <code>Dock_1</code> is clearly better.
  That's why I'm looking for better alternative than hydrogen bond.</p>
  <p><a href="https://i.stack.imgur.com/E1YcH.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/E1YcH.jpg" alt="enter image description here" /></a></p>
   12181: <p>maybe you can use the &quot;<strong>per-residue interaction scores</strong>&quot; (wich is available via Schrödinger).</p>
  <p>On the other hand,to show if a Docking Pose is really &quot;better&quot; you could show specific interactions rather than the complete big molecule.. e.g. an important salt bridge is missing. (hydrogen bonds are not that important, due to the fact that they can be bridged with water molecules)</p>
  <p>Sorry, this is not really a solution, but I am not allowed to comment jet -.-</p>
  