Hi everyone,

I'm performing redocking analyses and would like to know what is the most recommended or common approach for calculating RMSD when comparing the redocked pose with the original crystallographic ligand structure.

Specifically, should hydrogen atoms be included or excluded in this analysis? What are the justifications for each approach, especially considering that hydrogen positions in crystallographic structures may not be as well-defined as those of heavy atoms?

I am using the following command in pymol

align lig1 and not element H, lig2 and not element H, cycles=0, cutoff=0.0, transform=0

I would appreciate any insights, experiences, or references you could share on this topic.