If all you need to know is what structure associated with which sequence, the Multalign Viewer instance has an ‘associations’ attribute that is a dictionary of Molecule objects to Sequence objects.  Both of those objects have ’name’ attributes which could be printed out.  You don’t really describe what precise ‘association info’ you want to save, so I’m not sure if this meets your needs or not.  If not, let me know exactly what you want to save.

—Eric