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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
--
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