epitron Lv 1
It's hard to tell what direction you're manually pulling a protein because the force-vector doesn't look very 3D (you can't tell if it's coming towards you or going away from you).
A simple red/green 3D glasses mode might make it a little bit easier to distinguish.
Also, perhaps colours could be used to represent the Z-component of the force vector, by rendering a gradient (a bit like 3D fog). If the arrow is pointing slightly towards you, it will be lighter at the tip and darker at the base. If it's pointing slightly away from you, it will be the opposite.
