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Re: [modeller_usage] salign multiple structures, with an initial multiple sequence alignment

On 4/8/11 8:15 AM, Benjamin SCHWARZ wrote:

I clearly understand now it makes no sense to fix the alignment once
and forall, since the principle of the optimization algorithm indeed
relies on its modification :-) Still, would it make sense to feed
salign with an initial "hand-made" alignment ? If so, is it possible
and how to do it ?
Of course - whatever alignment you have when you run SALIGN is used as its initial alignment. 


Thanks also for the clarification of concepts between alignment and
superposition. As for the superpose() method you pointed out, I guess
it is the one from class selection since I see no other occurrence of
the "superpose" token in the doc.


Yes, that's the one.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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