[Biopython] Difference between SVDSuperimposer and PDB.Superimposer

[Hongbo Zhu 朱宏博]

http://en.wikipedia.org/wiki/Structural_alignment#Structural_superposition
On Fri, Nov 18, 2011 at 4:56 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

>
> Another question I have is if I use the C-alpha carbon of proteins,
> does it actually calculate the "real" rmsd, what I mean is -for
> instance, PYMOL would "throw away" atoms over several cycles to
> improve the RMSD, I don't want to do that--looking at the code I think
> bipython does calculate the "real" RMSD, is this correct?
>
>
Hi, George,

I believe when you said "real" RMSD, you actually meant the optimal
solution to the least squares problem. In SVDSuperimposer, SVD is employed
to solve the optimization problem given the correspondence between the
residues in the two structures. It always generates the optimal solution,
or the "real" RMSD with respect to the correspondence between residues. If
you change the correspondence between structures (like what pymol does
according to your description), it is like you have a different
optimization problem to solve. SVDSuperimposer does not change the problem
spontaneously. It solves the problem you input.

It seems that the PyMOL command you described is "align". Note that
"align" and "superimpose" do mean different operations, although they are
often (wrongly) used interchangeably.
 http://en.wikipedia.org/wiki/Structural_alignment#Structural_superposition
HTH
hongbo

Thank you very much,
> George
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-- 
Hongbo