On 10/24/11 11:04 AM, Benjamin SCHWARZ wrote: > 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 ?
No, feature 2 *is* the Euclidean distance, so W^2 designates both. To be more specific, W^2 is a matrix of residue-residue Euclidean distances. There is some scaling done internally so that all the features have roughly the same magnitude, but that's simply equivalent to changing the units of distance.
> 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 ?
Probably. One would hope that an alignment made using a distance matrix that is itself extracted from an alignment would reproduce that alignment, but it's not absolutely guaranteed.
Ben Webb, Modeller Caretaker