<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>

CC BY-SA 4.0
2021-06-01T09:11:29.183Z
Yup, spot on. `rsm_cur` is the correct command. One can pass the ligand w/o deleting: `rsm_cur redocked and resn LIG and not element H, original and resn LIG` if the residue name is `LIG` say, while the `not element H` is against hydrogens that were _added_ for docking. However, one *big* caveat worth mentioning is...
Matteo Ferla
CC BY-SA 4.0
2021-06-01T09:12:16.430Z
... is that the RMSD is segi, chain, resi, resn and name based (i.e.`alter`/`sort` operations may be required to make them match), has an isomorphism problem: Take BHT, if you flip it's "arms" 180° around the hydroxy–methyl axis, you end up with a perfect fit, but the atom names differ. So, one must make sure this is not an issue (or use RDKit).
Matteo Ferla
CC BY-SA 4.0
2021-05-31T15:13:14.757Z
2021-05-31T15:13:14.757Z
Lucas
<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>

<docking><pymol>
rmsd between re-docked complex and co-crystallized complex
# rmsd between re-docked complex and co-crystallized complex

(Asked by: username_0 on 2021-05-30)

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?

**Tags:** docking, pymol

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## 1 answers

### Answer by username_1 on 2021-05-31. Score: 1 | Accepted answer

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>)

> **Comments:**
> **username_2**: Yup, spot on. `rsm_cur` is the correct command. One can pass the ligand w/o deleting: `rsm_cur redocked and resn LIG and not element H, original and resn LIG` if the residue name is `LIG` say, while the `not element H` is against hydrogens that were _added_ for docking. However, one *big* caveat worth mentioning is...  
> **username_2**: ... is that the RMSD is segi, chain, resi, resn and name based (i.e.`alter`/`sort` operations may be required to make them match), has an isomorphism problem: Take BHT, if you flip it's "arms" 180° around the hydroxy–methyl axis, you end up with a perfect fit, but the atom names differ. So, one must make sure this is not an issue (or use RDKit).  

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