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