Re: [modeller_usage] [salign] concerning the manual : feature 2 and structure superposition

[Benjamin SCHWARZ <>]

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.)