Part I: Seperating Objects in the Scene w/ Volumetric Materials in question
The solution to this problem starts by assigning the volumetric objects (electron light trails) their own "Scene Layer" and corresponding "Render Layer" then using the "Mask Layer" to mask out the other "Scene Layers" containing any other objects, such as the nucleus, in the scene which you might want to include... like when the electron's orbit through or behind them which would naturally obscure the view of the trails.
Then in the "Object Properties Window" turn off the rendering of the offending surface objects (in this case the atom shells) that are causing the problems with the volumetric materials of the electron light trails.
- Next in the "Render Settings Tab" under "Shading" change the "Alpha Setting" from "Sky" to "Transparent". Then under "Output" make sure to set the "file format" as "PNG"; and, of coarse, it's always a good idea to save these files in their own folder, especially if you expect to have a bunch of files. And, don't forget to select "RGBA" so you have an alpha channel in your images, because you'll need to use alpha over in Blender's VSE in a separate blender file later. It's also a good idea to save this as its own file because you might want to use various compositing nodes, such as blur on your electrons and light trails.
You're now ready to render and save these images.
Part II: The rest of the atom (nucleus and shells)
- Once you've completed rendering the electrons and light trails "Save As" to create a separate file for the rest of the atom. Then go back to the "Object Properties" window and turn on the Rendering of the shells.
Next under the "Render Layers" tab select all the other "Scene Layers" and "Render Layers" and uncheck any "Mask Layers"... In my case I also chose to select the Render Layer containing the electron light trails and turned off rendering of the electrons and the light trails in the "Object Properties" Window.
In the "Render Settings" Tab under "Shading" change the Alpha Setting" from "Transparent" back to "Sky". Keep the "file format" as "PNG" with "RGBA" under "Output". And, don't forget to save these files in their own folder.
Part III: Composite Both Image sets in Blender's VSE
- Finally, its merely a matter of compositing both images in yet another Blender file. Add image set of the atom (shells & nucleus) to channel 1 and the electrons and light trails to channel 2 using Alpha Over as your "Blend Type" for the light trails. Select your favorite movie format, render and, your done. Beautiful!
Final Note: I noticed a lot of buzz concerning the new render engine "EEVEE" that's in the final phases beta development. For what ever reason... the gist I've gotten is that the developers are deciding to drop the original "Blender Render" from the Render Engine selection list... (via Blender Nation et. al). If that is indeed the case... What a tragedy! Why? It's a reaction rooted in my practical experience with both Cycles compared to Blender Internal. Sure, Cycles has much more power and a greater choice of options when it comes to materials than Blender Render. Even a knuckle draggin luddite, such as myself, who's still a relative Blender Newbee, can't argue against that. But, if the above project (this query on the above atom blend-file) is any evidence, albeit tenuous; my first few attempts to get the right look and feel of the materials began with using Blender Cycles. In short, I didn't like it. I just couldn't get the materials and their reaction to the ambient lights to "pop". So, I decided to try Blender Internal... After a few tries, I got what I was looking for. It came alive... It "popped". Granted, this may be because of my lack of experience with Blender... But, regardless of that, I suspect there are probably some things that would still come out looking better, when done in Blender Render. So, futile as it may be, I would ask those who's influence may be felt, to implore serious reconsideration of dropping Blender Internal as an option.
Consider this as an analogy: My electricity recently went out. Like some of you that may still have landlines, most if not all of these phones are VOIP. But, with no electricity you ain't got phone service because, VOIP's tied to the electrical grid. Old timers who still remember POTS, may recall that if your electricity blacked-out, you could still rely on plain ole telephone service to get through to the electrical company, because it wasn't tied to the grid... See where I'm goin with this?
Anyway, I figured I'd make a case for keeping Blender Internal, not just because of nostalgia but, because there's probably still a lot more we can still get out of this grand ole render engine, even if it hasn't been updated in more than half a decade.
Regardless of that, I still look forward to trying out Blender eevee upon its official release.