Hello all,

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?