1.

I used MatchMaker to align two structures, worked well and I got an alignment file-1.

Then I clicked on MatchAlign and got alignment file-2. 

The alignment-1 is different from alignment-2.

Could you please let me know what is the differnce between MatchMaker and MatchAlign?

2.

In the same function I can't find RR distance map. Is it applicable to MatchMaker/MatchAlign?

Thank you

Egor