[Biopython-dev] RMSD calculation

George Devaniranjan devaniranjan at gmail.com
Fri Oct 29 23:42:12 UTC 2010

Thanks Eric and Peter,
Your patience in answering this question is very much appreciated.
I think Eric maybe right, I tried the RMSD calculation for several
structures and VMD does give a lower value for them all.

Thanks once again for all of you for your answers

On Fri, Oct 29, 2010 at 10:39 PM, Eric Talevich <eric.talevich at gmail.com>wrote:

> On Thu, Oct 28, 2010 at 12:49 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()
>> In the code its says RMS-is RMS being calculated instead of RMSD???
>> I ask because VMD gives a different value for RMSD to the one from
>> Biopython
> Hello George,
> Here's my understanding of it:
> 1. RMSD and "RMS distance" both mean root mean square deviation, in terms
> of the distances in 3D space between each corresponding pair of atoms. The
> RMSD between all atoms in two aligned structures may be different than the
> RMSD between backbone atoms only. Or, if the two structures don't have the
> same peptide sequence, that raises another set of issues.
> 2. In Biopython, PDB.Superimposer internally uses SVDSuperimposer. It's a
> simplified wrapper.
> 3. The SVDSuperimposer module allows you to either (i) align two structures
> in 3D space and then calculate RMSD, or (ii) just calculate RMSD without
> spatially (re-)aligning the structures. PDB.Superimposer just does the
> former. If the structures weren't already aligned, these can yield very
> different values.
> 4. There are many ways to perform a structural alignment; SVDSuperimposer
> implements a simple one. PyMOL, VMD, ce, DALI, and other programs implement
> more advanced methods.
> So don't be alarmed that VMD gives you a smaller RMSD than PDB.Superimposer
> -- it just means VMD found a better alignment between the two structures.
> Best,
> Eric

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