I have two structure in PyMol, and each has one low-conserved loop that spans several residues between N-terminal conserved domain and C-terminal conserved domain. I have used align or super command. Only if I defined the full length residues, these two structure can be superimposed well, so I can calculate the RMSD for full length structure. Is it possible to calculate the RMSD just between these two low-conserved loop?
Any answer is welcomed，thank you very much！