[Biopython] Difference between SVDSuperimposer and PDB.Superimposer

[Robert Campbell]

Hi George,

On Fri, 2011-11-18 10:56  EST,  George Devaniranjan
<devaniranjan at gmail.com> wrote:

> Hi,
> 
> I would like to calculate the RMSD using biopython, there seems to be
> 2 functions ( SVDSuperimposer and PDB.Superimposer) I could use, is
> there a difference?
> 
> 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?

You can, of course, prevent PyMOL from rejecting atoms, by telling it to
only do a single cycle (command line option: "cycles=1").  If you want to do
batch aligning of many structures, you can also use a script that will do
the alignment without starting up the graphics.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<robert.campbell at queensu.ca>    http://pldserver1.biochem.queensu.ca/~rlc