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There is a webapp which uses Java & ActiveX and it gladly accepts most keyboard shortcuts, but IE will intercept certain ones like F3 and Ctrl+Shift+F.

Can IE keyboard shortcuts be changed or disabled in some setting or file somewhere?

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In the JQuery hotkeys docs the venerable John Resig states that IE will, "let you handle built-in short-cuts, but will add their functionality after your code has executed."

Could the app be receiving the keystrokes in addition to IE?

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This may be true for JQuery stuff, but regular HTML accesskeys will not be executed if they match a shortcut in IE. For example, alt-d selects the address bar, so you can't use accesskey='d' for any HTML form buttons or links. – NReilingh Jun 29 '12 at 14:06

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