[Biopython-dev] RMSD calculation
devaniranjan at gmail.com
Thu Oct 28 17:14:44 UTC 2010
x, y being arrays-I took this from the example/comment section of
super_imposer = Bio.PDB.Superimposer()
print "RMS( using PDB superimposer ) = %0.4f" % ( super_imposer.rms)
(I took this from the Warwick example and modified for my use)
Yes there is a difference-for 2 proteins having exact same residues of 36
residues the values from 4 sources are as follows
SVD RMSD =3.2
>From the EU Bioinformatics server (link below) RMSD =1.75
So Biopython really is computing the RMSD and not RMS?
On Thu, Oct 28, 2010 at 1:04 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:
> 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
> > I ask because VMD gives a different value for RMSD to the one from
> Very different? There are bound to be some floating point differences.
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