Is there some user friendly software out there that I can punch a protein sequence into...

Question

and it will make an attempt at calculating the 3D structure, so that I can have a good indication as to whether sticking a few amino acids on the N/C termini will affect the tertiary structure.

Answer 1

It won't let you pick, but Folding at Home is a nice program that lets you see protein folding in 3D.