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 "the best" set of corresponding atoms. This is what SSM (or GESAMT) does and it cannot be guaranteed that a an atom in one chain will have a match in another chain. Note that alignment != best rms superposition. Eugene On 12 Sep 2014, at 14:45, KAUSHIK H.S. wrote: 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 when the topology is not closely related. For now, I do SSM superpose, identify the residues, explicitly mention them in LSQKAB program and then calculate RMS for each position. However, is there a way we can make SSM calculate RMS for all positions? Or, Is there a program which will give all atom RMS for a previously superposed protein structure ensemble? Thanks, Kaushik, Molecular Biophysics Unit, IISc, India -- Scanned by iCritical.