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I'm currently using UltraVNC to connect to my Mac Mini from my Windows 7 machine. I'm running into annoyances/issues because I'd like to use activate certan Mac key combinations from my Windows keyboard but can't, and I may even want to remap explicitly what Windows Shift, Alt, Ctrl, and Win do on the Mac when I'm using the VNC client.

Does anyone know if it is possible to customize this in UltraVNC, or if there is some other client that can do that?

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Did you check what the keys are actually mapped to? Shift and Control should be mapped as they are, but Alt is usually mapped to Cmd on the Mac side, so it might be that you don't have any key mapped for the Mac's Alt. I myself am looking for a way to map Windows key to Alt key on Mac while connecting from ubuntu using vinagre. Since you are on windows, you might find this thread useful in which one one of the answers states that the alternative vine server has this mapping correctly setup. I didn't like how slow the vine server is, so I use xvnc for its improved clipboard support over the built-in vnc server.

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