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
