Structure mode, Hotkey '2', changes the puzzle to be able to accept changes to the structure. Each segment of a protein can have one of three structural assignments, Sheet, Helix or Loop. These structures are a reflection of the geometry the backbone segment has. Assigning a structure does not impart any forces on the segments, though, it might seem that way at times. For example, in attempting to rebuild a section as a helix, you might have no success. Then, after setting the segment section using the Structure Mode to Helices, the section zips right into a helix formation. It might seem as though the structural setting applied forces on the segments but all it did was to present the rebuild with more helical geometry points to choose from than others.