[Biopython-dev] RMSD calculation

[Peter]

On Thu, Oct 28, 2010 at 6:14 PM, George Devaniranjan
<devaniranjan at gmail.com> wrote:
> Yes there is a difference-for 2 proteins having exact same residues of 36
> residues the values from 4 sources are as follows
> VMD RMSD=1.61
> SVD RMSD =3.2
> PDB RMSD=3.2
>
> From the EU Bioinformatics server (link below) RMSD =1.75
> (http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver)
>
> So Biopython really is computing the RMSD and not RMS?
> Thanks you

It has been a while since I looked at this (but I can still edit
the Warwick page if is is unclear).

Which definition of RMSD are you using?

Bio.PDB uses Bio.SVDSuperimposer, so they should be the same.
The comment for this code *says* is calculates the RMS deviation,
here:

        diff=coords1-coords2
        l=coords1.shape[0]
        return sqrt(sum(sum(diff*diff))/l)

Here variable l will be the number of atoms.

What are the two examples you are using? Can you at perhaps
share a small example pair of PDB files?

Peter