I don’t know if this idea has been posted yet, but I was wondering if, in addition to displaying the energy for all structures, perhaps also the ability to only display the energy for specific structures, such as loops. Also, perhaps the ability to display the sum of the energies in a stack, Instead of displaying -1.4, -1.3, and -1.4, it would instead be -4.1. This would be useful in solving puzzles, as it would show whether a stack’s sum total negative energy is great enough to be stabilized next to a loop’s positive energy. Thanks for the game. 
I second this idea very much, as it would be easier to see also if there is a relatively even energy distribution in a design too.
Summing up the stacks sounds very counter-intuitive to me so i’d leave that as an option only. Would it be possible to apply “stitches” to red sections of a puzzle so when switching between natural and target mode these sections don’t switch and keep their energies in target mode? This is the interface identical solution to GC’ing your puzzle. You’d click on a pair that’s in a red section, and that whole section gets stuck in target shape. Your shape is still red, so you can’t submit, but it won’t come apart and get it’s energy recalculated, so you can work in sections.
Since we’re only stitching target shape, 4 numbers could store any stitch (first and last white shape bases of each strand), and if any of these 4 bases misfolded the stitch can be invalidated temporarily and energies calculated normally. This would allow the stitch to only stick of it’s surroundings do.
Similar method looking at it from another angle is to select a pair and then display the energy of the red section around it in a small secondary window, again calculated from the nearest 4 white bases in the shape (or 2 if hairpin). This would also allow clicking on a white stack and get it’s total energy the same way.