Hi Ben,
And thank you for that fast answer, as usual :)
> Given that you don't say what you think it might mean, all I can do is restate it and hope it makes more sense. ;)
I didn't expect less… I was really lost ;)
> To calculate feature 2, the Euclidean distance between residues in two structures, the structures must be aligned. So SALIGN does this, but that alignment is only a temporary one; it is used only to determine the values of feature 2. The final alignment is done in the regular way, by dynamic programming using *all* features.
Actually, I think I was able to see clearer thanks to your restatement.
I think it is a matter of juxtaposed terminology and symbols : W^2 designates feature 2, not the Euclidian distance; and W designates the global cost function (the one that uses all features).
Correct ?
So basically, what you told me here, is that the computation of W2 produces another (and temporary) alignment, used to produce a superposition of structures (again a temporary one).
Just to enforce my understanding : What would happen if I set all features to 0 except for feature 2 ? would the two superpositions be the same ?
--Ben( S.)