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I'm using emacs gui on gnome-shell(3.2). I just set transparent background as the guide shows. It actually works on xfce4 (with compositor turned on). But failed on my gnome-shell laptop.

So is there any workaround on gnome-shell to support this feature?

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Gnome Shell (Gnome3) uses the Mutter window manager. There is a bug report about "No opacity in emacs with mutter". Possibly the bug reporter means transparency, not opacity, because this text appears in the bug report: "No transparency at all with mutter."

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