[BiO BB] rmsd calculation

[Sourangshu Bhattacharya]

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
neighbour.

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 !!!

Sourangshu

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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