As I found, there is no way to set opacity/transparency for the representation, while it is important when you make visible two or more representations in the same time, especially for the surfaces and sometimes for cartoon. As an example, there's my scene made with NGL:
Its still WIP, but I think concept is clear - my goal is to show displacements of sidechains after some modification while user should keep in mind structure's cartoon
The same is about surfaces, sometimes you need see surface and cartoon together which is easier when surface is partially transparent
As I found, there is no way to set opacity/transparency for the representation, while it is important when you make visible two or more representations in the same time, especially for the surfaces and sometimes for cartoon. As an example, there's my scene made with NGL:
Its still WIP, but I think concept is clear - my goal is to show displacements of sidechains after some modification while user should keep in mind structure's cartoon
The same is about surfaces, sometimes you need see surface and cartoon together which is easier when surface is partially transparent