I have a question about structure comparison, I usually use Matchmaker to overlap 2 similar protein fragment to compare the difference. I wonder if the structure is bent or twisted during the matching process, in order to fit the reference structure more?

For example, the attachment is for demonstration. 

There is a protein A, and protein A have a short from that miss some amino acid (the green part is missed). So the result produced by the Matchmaker would be A or B?

If the result is A, can I make result B by UCSF Chimera?

Thank you!