[Biopython-dev] RMSD calculation

Peter biopython at maubp.freeserve.co.uk
Thu Oct 28 17:04:53 UTC 2010

On Thu, Oct 28, 2010 at 5:49 PM, George Devaniranjan
<devaniranjan at gmail.com> wrote:
> I was wondering why there is two functions for calculating RMSD
> 1)in the SVDSuperimposer()
> 2)in PDB.Superimposer()

Can you clarify? There is no function in Bio.PDB.Superimposer to calculate
RMSD (or RMS), but it does call the Bio.SVDSuperimposer module internally.

> In the code its says RMS-is RMS being calculated instead of RMSD???

There could be some confusion in the comments about root mean squared
(RMS) *deviation* (i.e. statistical standard deviation) versus RMS *distance*.

> I ask because VMD gives a different value for RMSD to the one from Biopython

Very different? There are bound to be some floating point differences.


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