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
