Dear all, I have 2 queries regarding RMSD calculation and interpretation.
1. When 2 residue stretches are superposed using CCP4 superpose, the log file shows the atomwise-deviations between matched residue pairs. How to find the total deviation/RMSD between a specified residue pair - should the RMSDs of the individual atoms be summed over, or is there some other formula? 2. Residues are not static; this dynamic nature is evident from variations (for a given residue; by variations, I mean that the residues don't superpose completely) when multiple chains of the same structure (from multiple chains in AU of a PDB, or from different PDBs) are superposed. My question is: is there an RMSD cut-off below which the variation can be considered as thermal fluctutation, and above which they can be said to be a different 'conformation' or 'state'? Thanking all, regards, ansuman
