[BiO BB] superimposition trouble

[Rakesh Motani]

Hi, I am a new user for SwissPDB viewer. I am trying to superimpose 2 
structures. They have almost same sequence just 1amino acid difference. 
Before superimposing (ie using fit--> itterative magic fit command) I 
can see that both are same. After using the fit command I mentioned part 
of the second sequence in superimpostion disappears and they don't fit 
well. I would be great if Ican get some suggestions on this. I thinks 
it's a software issue.
John