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

Regards

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