When we use the Superimpose Proteins Tools for superimposing protein structures based on sequence alignment, the superposition is performed on all the residues that are aligned in the sequence alignment window.

We can also carry out the superposition using only a select set of residues, such as the binding site residues. All we have to do is to select those residues in the reference protein in the molecule window (or in the sequence window), before clicking the Superimpose button. Any residues aligned with the selected residues in the reference protein will be used for superposition. Click on the Show Report button to see the report of how many residues are used to perform the superposition.