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I found that the user interface of Skype is not aligned with the Unity theme and lives its own life. Trying to play with the options in Skype, Qt3 and Qt4 didn't lead to any result. How do I make Skype integrate with the system theme in Ubuntu 11.10?

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There is little you can do about this, because Qt 4 does not yet have support for integrating with GTK+ 3.x. For this reason, Skype will look out of place until either Skype switches to another toolkit, or until Qt gets support for GTK+ 3.x themes, or until someone comes up with a program to get the colour scheme from GTK+ 3.x and apply it to Skype.

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