I have generated five models for a protein and I
wanted to check the RMSD of only the binding site residues. I have the list of binding site residues. I tried using this through graphics by selecting the residues and then aligning by selection but somehow its giving me a higher RMSD than the entire structure but this should not happen. What is the other way to align specific residues?
Senior Research Fellow
Sri Venkateswara College
(University of Delhi)