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

[Benjamin SCHWARZ <>]

Dear modellers, 

	Reading the salign documentation (http://salilab.org/modeller/manual/node300.html) I have troubles understanding a specific paragraph concerning feature 2. The paragraph is the following :

<< The alignment produced within the routine that calculates W^2 does not generally correspond to the alignment calculated based on W. Therefore, the multiply superposed structures are not necessarily superposed based on the final multiple alignment produced by alignment.salign(). If you wish such a superposition, you can use alignment.malign3d() with fit = False and write_fit = True (the meaning of fit is different between alignment.salign() and alignment.malign3d()). >>

And since I am kind of really lost on the interpretation, any clue is welcome.
   Thanks

	--Ben( S.)