Alpha channel in representations

[tam10]

Transparency in molecular representations could allow comparisons between large geometries such as proteins and nanotubes in chemical reactions, optimisations etc.

For entire representations, it's fairly easy to allow transparency by adding:
transparent: true, opacity: alpha
to the THREE material's arguments. However, a bit more effort would be needed to control individual atoms, but I can't think of a situation where varying transparencies could be useful.

For now, if it seems useful, I can add an opacity option for balls_and_sticks and isosurfaces.

[gabrielelanaro]

I think that's a pretty good idea, yes we can stick with a per-representation alpha value as there's probably not much use for a per-atom alpha value