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Problems with Povray and transparent background

Dear users

I’ve been playing around with Avogadro and I wanted to export structure with a transparent background. But from my understanding, the only way to do it is with Povray. But exporting with PovRay gives me two problems.
1st - Shows some shadow of the structure in some atoms. Is there a way to remove this?
2nd - It cuts part of the structure for some case I do not get it. Is there a way to render the full structure?

Hi! What version of Avogadro are you using? I am not a pro in PovRay, but I guess version can be important. Regarding the 1st question, PovRay should make shadows, this is the part of what it is designed for.
If you just want a picture with transparent background my suggestion is to set some untypical background color (like chromakey) and then make this color transparent in the final image using some image editor (GIMP will do).