On 4/7/11 9:20 AM, Benjamin SCHWARZ wrote:
Trying to align several structures of a similar domain, I have a "hand-made" sequence alignment for these domains. Is it possible to ask salign to use this initial sequence alignment ? Is it possible to ask salign to keep that same multiple sequence alignment unchanged during the whole process ?
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 -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage