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

[Benjamin SCHWARZ <>]

> If you don't want to change the alignment, then there's not really a "process" going on here (since the "process" is optimizing the alignment by means of dynamic programming). It sounds like what you want to do is superpose several structures based on an existing sequence alignment. You want superpose(), not salign(). Note that superpose is only pairwise though, so you'll have to run it in a loop.
> 
> 	Ben Webb, Modeller Caretaker

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 ?

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.

    --Ben.S