Switching around between the Crtl+Shift+B mode and Crtl+Shift+M to see everything doesn't seem to be the most effective way.
Form of the sidechains at the moment isn't used as an vehicle to display information apart from displaying where an atom is positioned.

I added a rough sketch of of a negativly charge that's at the moment displayed in blue in the Crtl+Shift+B mode and a positive charge could be displayed.
Additionally I also sketched a way to show sulfur that's based on form.

Providing more information about the protein will increase the chance that people will detect pattern through intutive processes.