I'm using the tool MatchMaker to align different structures. 

My reference protein has 3 domains very similar and I would like to show an alignment of other 3 proteins with each one of those 3 domains. The problem is that the 3 protein always align to the same domain (one of the 3, instead of each one with a different domain).

How can I do so I can exclude the part of the protein already aligned in new alignments?

I hope I explained myself and thank you in advance.

Francisco Benitez.