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

On 10/24/11 7:18 AM, Benjamin SCHWARZ wrote: > Reading the salign documentation > (http://salilab.org/modeller/manual/node300.html) I have troubles > understanding a specific paragraph concerning feature 2.

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. ;) 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.

Ben Webb, Modeller Caretaker