Answers.Body: <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>
  
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Answers.Text: Totally. To further this, a salt bridge contributes something like -2.5 kcal/mol, while a h-bond -1 kcal/mol. pi-pi bond or S-pi about -1 kcal/mol, but that does not account for the improved solvatation term, which plays a role.  Coordinated waters play a massive part in many protein, e.g. G-protein alpha–beta interaction, ribosome, barnase-barnstar etc., and a water can contribute some -3 kcal/mol.
Answers.UserDisplayName: Matteo Ferla
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Answers.Text: @MatteoFerla my key concern is to show that *visually*.  Is there  away I can show salt-bridge, pi-pi bond, S-pi bond with Pymol to show the difference of two docking?
Answers.UserDisplayName: neversaint
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Answers.Text: @Lucas thanks. Is there a way to show "per-residue interaction scores" visually in Pymol? Is there away we can systematically identify **specific interactions** that matters? Any reference on this? I appreciate your reply.
Answers.UserDisplayName: neversaint
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Answers.Text: @MatteoFerla Also, if I want to show salt-bridge with Pymol. What's the reasonable residue to choose from each ligand and receptor?
Answers.UserDisplayName: neversaint
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Answers.Text: Your `E` looks like a ∆∆G in kJ/mol, which means that they were docked with a forcefield method. You may have among the files a per-residue split of the forces.
  For PyMOL, `select salty, ((byres (resn ASP+GLU around 3)) and resn LYS+ARG) or ((byres (resn LYS+ARG around 3)) and resn ASP+GLU)` should work for salt bridges btween canonical amino acids.
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Answers.UserDisplayName: Lucas
Body: <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.sstatic.net/E1YcH.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/E1YcH.jpg" alt="enter image description here" /></a></p>
  
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Comments.Text: In the last paragraph of this post are some suggested things to check that may be useful: https://bioinformatics.stackexchange.com/questions/16192/how-to-calculate-rmsd-and-binding-energy-from-the-already-docked-ligand-receptor
Comments.UserDisplayName: Matteo Ferla
Tags: <protein-structure><pdb><docking><pymol>
Title: How to show that one docking is better than another with Pymol visually
ThreadText: # How to show that one docking is better than another with Pymol visually
  
  (Asked by: username_0 on 2021-07-08)
  
  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.
  
  [![enter image description here](https://i.sstatic.net/E1YcH.jpg)](https://i.sstatic.net/E1YcH.jpg)
  
  **Tags:** protein-structure, pdb, docking, pymol
  
  > **Comments:**
  > **username_1**: In the last paragraph of this post are some suggested things to check that may be useful: https://bioinformatics.stackexchange.com/questions/16192/how-to-calculate-rmsd-and-binding-energy-from-the-already-docked-ligand-receptor  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2021-07-08. Score: 1
  
  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 -.-
  
  > **Comments:**
  > **username_1**: Totally. To further this, a salt bridge contributes something like -2.5 kcal/mol, while a h-bond -1 kcal/mol. pi-pi bond or S-pi about -1 kcal/mol, but that does not account for the improved solvatation term, which plays a role.  Coordinated waters play a massive part in many protein, e.g. G-protein alpha–beta interaction, ribosome, barnase-barnstar etc., and a water can contribute some -3 kcal/mol.  
  > **username_0**: @username_1 my key concern is to show that *visually*.  Is there  away I can show salt-bridge, pi-pi bond, S-pi bond with Pymol to show the difference of two docking?  
  > **username_0**: @username_2 thanks. Is there a way to show "per-residue interaction scores" visually in Pymol? Is there away we can systematically identify **specific interactions** that matters? Any reference on this? I appreciate your reply.  
  > **username_0**: @username_1 Also, if I want to show salt-bridge with Pymol. What's the reasonable residue to choose from each ligand and receptor?  
  > **username_1**: Your `E` looks like a ∆∆G in kJ/mol, which means that they were docked with a forcefield method. You may have among the files a per-residue split of the forces. For PyMOL, `select salty, ((byres (resn ASP+GLU around 3)) and resn LYS+ARG) or ((byres (resn LYS+ARG around 3)) and resn ASP+GLU)` should work for salt bridges btween canonical amino acids.  
  
  ---
  
  