[BiO BB] rmsd calculation

Sourangshu Bhattacharya sourangshu at csa.iisc.ernet.in
Sun Sep 19 11:32:56 EDT 2004

Hi Pankaj,

I believe you are having problem in finding out the equivalences.
Generally, a nearest neighbour approach is very intuitive. That is you say
that one residue has been equivalenced with it's nearest spatial

However, it is not guarranteed to be symmetric. That is, a is NN for b
doesn't mean b has to be NN for a. You can use any heuristic there.

After this RMSD calculation is just computation !!!


On Wed, 15 Sep 2004, Pankaj wrote:

> Hi all,
> I have a pdb file of 2 superimposed structures. I want to know the
> rmsd of a part of 1 structure to a part of the 2 structure. For this
> rmsd calculation I dont want to disturb the superimposition. how do I
> do that?
> thanking all in advance
> Pankaj Kamra
> Research Scholar
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