Thanks Eric, it works. To summarize:
#----------------------------------------------------------------------
def findMAV():
from chimera.extension import manager
from MultAlignViewer.MAViewer import MAViewer
mavs = [inst for inst in manager.instances if isinstance(inst, MAViewer)]
if not mavs:
raise AssertionError("No MAV instances")
return mavs[-1]
#----------------------------------------------------------------------
mav = findMAV()
mav.saveAssocInfo('myfile.asc')
#----------------------------------------------------------------------
Best
Hernando