When using the Ideal SS tool, the lower-numbered end of the backbone piece always moves and the higher-numbered end always stays in place. Half the time this is the opposite of what I would choose. Please let us choose which end will stay in place by freezing it.
(changed to Game Tools topic)
You can always cut both ends of the piece whose structure you are trying to idealize, and then manually move the structure back to a place where you can reconnect the ends. More often than not, you will need to rebuild one of the connecting loops, either of the cut piece or the piece adjacent, to make both ends neatly meet.