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
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