# rmsd between re-docked complex and co-crystallized complex

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?

• 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... Jun 1, 2021 at 9:11
• ... 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). Jun 1, 2021 at 9:12