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