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I'm trying to enable tap to click from a bash script using:

defaults write com.apple.AppleMultitouchTrackpad Clicking -int 1

When I open the Trackpad section on the System Preferences panel, the checkbox is disabled for the setting but it is working. I can tap to click.

What do I need to change in order to show that the setting has been modified in the System Preferences panel?

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The property Clicking is a boolean value.
The property list is read at login.
If the System Preferences dialog is open when the property is set via the defaults write command, it could silently fail.
Apart from the com.apple.AppleMultitouchTrackpad.plist file, the same property is used in com.apple.driver.AppleBluetoothMultitouch.trackpad. I'm not sure if you are using the external Trackpad, but no harm in setting both values.

So for good measure I do:

osascript -e 'tell application "System Preferences" to quit'
killall cfprefsd
defaults write "com.apple.AppleMultitouchTrackpad" "Clicking" -bool true
defaults write "com.apple.driver.AppleBluetoothMultitouch.trackpad"  "Clicking" -bool true

And then just logout and back in. :)

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