[Biopython-dev] RMSD calculation

[George Devaniranjan]

Hello everyone,
I tried with pymol and it gives a value of 1.792 for the RMSD after
alignment
The EU bioinformatics server gives a value of 1.74
VMD 1.62
But SVD and PDB Superimposer gives a value 3.2
I have attached the 2 PDB files concerned-is it something I am doing in
calculating the RMSD using biopython?
Thank you

On Thu, Oct 28, 2010 at 1:46 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> 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
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: protein1.pdb
Type: chemical/x-pdb
Size: 16983 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biopython-dev/attachments/20101028/f92a9d96/attachment-0002.pdb>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: protein2.pdb
Type: chemical/x-pdb
Size: 16981 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biopython-dev/attachments/20101028/f92a9d96/attachment-0003.pdb>