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?