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I am starting a screen session with screen /dev/ttyACM0 115200. The system I am opening a session to is running Ubuntu, and I would like to pass it Ctrl-Alt-F1. How can I make screen capture those keystrokes and send it to the system?

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screen does not know anything about CtrlAltF1. It only knows about sequences of bytes. The CtrlAltF1 may have meaning to a terminal emulator in which you are running screen (and send an interesting sequence of bytes to the application), but its meaning may be (as in a Linux virtual console) be built-in in a manner which prevents the key from sending data to your application.

For instance, the Linux Keyboard and Console HOWTO says that this combination will switch to virtual terminal number 1.

According to How to disable Ctrl + Alt + Function key combinations on Debian?, you can disable the switching while running in X, while How to disable “ctrl + alt + Fn” shortcut? gives similar advice while cautioning that doing this will disable other useful features.

Finally, Rebinding/disabling CTRL+ALT+F# gives more examples.

None of those give any clue regarding what bytes might be received by an application once the configuration is changed, though the referenced comments in DontVTSwitch doesn't pass through Ctrl-Alt-(Shift)-Fn to applications claims that it works.

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