Dear Sreetama, I use an ancient superposition program which rejects all atom pairs deviating more than 3 sigma and repeats this procedure until convergence. It then reports the RMSD for all atoms and for the atoms deviating less than 3 sigma. I find this an excellent method to separate the core from variable loop regions. It also ensures a robust superposition of the cores, ignoring variable loops.
Best, Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von sreetama das Gesendet: Mittwoch, 13. August 2014 08:12 An: [email protected] Betreff: [ccp4bb] RMSD between structures of homologous proteins Dear all, When calculating the RMSD between structures of homologous proteins, where there are large changes in the loop region(s), which RMSD should be reported - an overall value which may be inflated due to the deviations in the loops, or separate values for the core and loop regions? What is the best way to calculate the RMSD for superposition of the cores - should I prepare a separate PDB file by removing the coordinates of the loop residues and then superpose? Thanks in advance, Sreetama das, PhD student, Physics, IISc
