[phenixbb] alternatives to RMSD

Dmytro Guzenko dmytro.guzenko at pharm.kuleuven.be
Thu Jul 3 04:09:08 PDT 2014

Hi Patrick

Take a look at the Binet-Cauchy kernel, e.g. here: 

It is a shape-correlation metric that is rather insensitive to global 
shape changes, but sensitive to local ones. Maybe that's what you need. 
It's also much faster to compute than RMSD.

I have attached a python code snippet that computes a BC distance matrix 
for a set of proteins defined by CA coordinates.

Kind regards,

On 02/07/14 17:15, Patrick. C wrote:
> Hi Phenix users,
> I am not a crystallographer but I though you guys might be a good 
> place to ask this question.
> I have 2 super secondary structures, A and B and they consist of 
> Helix-turn-Strand
> Due to the turn the two structures have a poor RMSD because the two 
> flanking fragments of Helix and Strand are far from each other but 
> when I superimpose the two fragments individually(helixA with helix B 
> and standA with strandB in Pymol they align very well).
> Now, is there a way to express this instead of using the RMSD?
> When the two structures align well the RMSD is very good but a slight 
> movement and the RMSD is awful.
> But looking at the two structures I can see they follow the same path 
> through space.
> Thank you,
> Patrick
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