[Chimera-users] Realign sequences

[Hernando J Sosa]

Is there a way to realign sequences already in a multialign window within a python script?
I want to do this because the first alignment dome using matchmaker in many cases contains mismatches to the aligned structures. Using the realign option in the menu fixes the problem but I want to do this within a script.

I have code that creates the alignment window and then retrieves the instance:

from chimera.extension import manager
from MultAlignViewer.MAViewer import MAViewer

runCommand('mm #0 #1 show true')
mavs = [inst for inst in manager.instances if isinstance(inst, MAViewer)]
mymav = mavs[-1]

I tried then to do something like
mymav.realign()

However, I don't  know what parameters to put in the realign function, or whether this is the right function to use or whether there is a better way to do this.

Any help would be appreciated

Thanks

Hernando


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