I don't want to model one fragment of a protein. I want to achieve
this by using the "\" sign in the alignment, but I'm not sure how the
pir file should look after insertion of the "\" sign. Should it look
like this:
You're close, but you need to make two changes:
1. It's the '/' sign, not the '\'.
2. Since a chain break denotes a break *between* two residues, it has
zero width. It doesn't make sense to align a chain break with a 'real'
residue; you need to align it with either another chain break or a gap.
So in this case you probably want to add a gap to your template: