At the start of a new game the beginning state of the protein is centered in the frame along with the gray guide. If you don't see them hit "Home" or "Q" keys to recenter the view. As a protein is disturbed by a tug or a script, the backbone changes shape, wiggles and turns all about. This at times causes the protein to travel away from the center of the frame. The gray guide can be turned on/off in View menu.