text: user12372: I would like to calculate the rmsd between re-docked complex and co-crystallized complex for docking validation. How do I calculate the rmsd using Pymol? I tried the following command
  align re-docked_complex, co-crystallized_complex
  
  But the above command gives the rmsd of two proteins. I would like to get the rmsd of re-docked and co-crystallized ligand. How can I achieve this using pymol?
  
  user12181: Welcome.
  The Protein-Ligand-complex is the complete protein with Ligand!
  If you only want to compare the two ligands, you can delete the rest of the proteins, or specify the input so only the ligand is choosen. (select Ligand and save selection. then use the function on that selections)
  But be aware that for Docking comparison you probably don't want to align! but rather calculate the RMSD directly (because the absolute position and not the relative position is of interest?)
  Maybe use: "rms_cur" (https://pymolwiki.org/index.php/Rms_cur)
  
original_text: 12372: <p>I would like to calculate the rmsd between re-docked complex and co-crystallized complex for docking validation. How do I calculate the rmsd using Pymol? I tried the following command</p>
  <pre><code>align re-docked_complex, co-crystallized_complex
  </code></pre>
  <p>But the above command gives the rmsd of two proteins. I would like to get the rmsd of re-docked and co-crystallized ligand. How can I achieve this using pymol?</p>
   12181: <p>Welcome.</p>
  <p>The Protein-Ligand-complex is the complete protein with Ligand!</p>
  <p>If you only want to compare the two ligands, you can delete the rest of the proteins, or specify the input so only the ligand is choosen. (select Ligand and save selection. then use the function on that selections)</p>
  <p>But be aware that for Docking comparison you probably don't want to align! but rather calculate the RMSD directly (because the absolute position and not the relative position is of interest?)</p>
  <p>Maybe use: &quot;rms_cur&quot; (<a href="https://pymolwiki.org/index.php/Rms_cur" rel="nofollow noreferrer">https://pymolwiki.org/index.php/Rms_cur</a>)</p>
  