Hi,
I want to calculate main-chain and side-chain deviations between sets of
identical proteins modeled into different 3D structures. While SSM superposes
well, it calculates RMS only for the residues considered for superposing.
Though LSQKAB program calculates RMS for all positions, fails
This problem cannot have an ultimate solution unless your chains are of the
same length and you postulate that residues should be corresponded one-to one.
But if this is the case, LSQKAB is the tool.
If correspondence between C-alphas is ambiguous, you need to align structures
in order to find
