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I usually swap control and capslock, but the old Laptop I am using has no win key which I use as a Super key.

So that is why I would like to have to assign Control_L to caplock but control to Super_L

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You can use the following commands:

xmodmap -e "keycode 66 = Control_L NoSymbol Control_L" #this will make Caps_Lock key to act as Control_L
xmodmap -e "keycode 37 = Super_L NoSymbol Super_L"     #this will make Control_L key to act as Super_L

To make these changes permanently, see this answer.

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Does not work, xev shows that your mapping is correct, but if I use control(capslock)-k to kill a line in a shell it does not work, while (control-k works, although xev tells me it should be super, very odd –  user224199 Dec 11 '13 at 23:12
    
I also thought this should work, but it doesn't. Would be grateful for any pointers. –  Shay Jan 18 at 22:58
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