So here is a molecule that I chose, Neuropeptide F
Basically you create a unit that you copy again and again. Choose your color and create someting like this in one layer. This first layer is going to be our front of the molecule.
Group your first unit and copy it few times. It looks better when each new copy gets under the previous one. Also you can shuffle few subunits so it doesn't look exactly the same.
Now group the whole thing. This is going to be the main helix of the molecule - front turn, if you like. Copy it few times - as many times as many turns you want.
Now we are going to create the back of the molecule. Create new layer "back" and put it under the front one. Now copy one front turn to the back layer. Copy it one more time so you have two on the top of eachother. Select the top one and click "Unite" in Pathfinder tab.
Change the color of the united sub-layer to black and adjust the opacity to for 20%. Or less. Or more. As you please. You are done with the unit that is going to create the back turn.
Now group the whole "back turn" thing and copy it so it connects the turns.
The you just copy it few times as you like. Then you take front turn subunit, shuffle it and start to create the rest of the molecule.
You can also add some smaller units (aminoacids) that stick from your molecule. Aaaaand you are done with your own beatifull neuropeptide F.
