RMSD for individual residue

From: gurunath katagi (gurukatagi_at_gmail.com)
Date: Mon Nov 30 2009 - 11:55:34 CST

Dear all,
I am calculating the average RMSD over time of each residue in a protein
molecule which has multiple chains (four ).(RMSD for individual residue
using residue_rmsd.tcl)
My question is whether we need to calculate the Average RMSD of each residue
for each individual chain or take it has whole (four chains ).

Because , when i did by both methods (taking the RMSD chain wise or as a
whole), i am getting different RMSD values for each residue . I am not
getting why there is a difference for individual residue and whether i need
to take the RMSD for individual residue at once or chain wise ?

Thank you

Gurunath M Katagi
Graduate Research Student
Bio molecular computation Laboratory
Supercomputer Education & Research Center
Indian Institute Of Science, Bangalore- 560012
Karnataka State, India
email: gurunath_at_rishi.serc.iisc.ernet.in

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