regarding the density of your thickened pipe, i am not sure what to suggest since i have absolutely no idea how that could look like. from my understanding is that you are dealing with molecules whos atoms are connected through electrons and line up to this genes. so actually there is not much to display, a pipe could do but if you say its too dense then i have to ask what you are trying to show and maybe there is a better way… will this be animated? to which detail will you show it? maybe using kind of a translucent cloud instead of a pipe could work. interesting topic of course, i am not very educated in it unfortunately.
you can also use a dotted line
or underlay it with a line on another layer and play with the thickness/visibility
but that all depends of course where you will render it and if its animated.