Dear Sir/Madam

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?

Thanking you


Nidhi Jatana
Senior Research Fellow
Bioinformatics Center
Sri Venkateswara College
(University of Delhi)
Dhaula Kuan
New Delhi-110021.