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.
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