I want to calculate RMSD for my docking protein models. So I have one target
model and one docked model. Each model has a larger chain called receptor,
and a smaller chain called ligand. The chains in docked model is highly
sequentially similar to the corresponding chains in the target model.
I want to calculate two RMSDs. One is the RMSD for ligands. I want to
superimpose the receptors in target and docked model, and then calculate the
RMSD for ligands. The second RMSD is RMSD for interfaces. I want to
superimpose the interfaces of target and docked model, and calculate the
RMSD for the interfaces.
Since the chains have a high similarity, I should use align command instead
of super command, right?
If I use align, could someone tell me how I can get the two RMSDs?