[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:
http://bioinformatics.oxfordjournals.org/content/30/6/784.long
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,
Dmytro.
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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