For example, my new settings are these :
Shift : Shift_L Shift_R
Lock : Caps_Lock
Ctrl : Ctrl_L
Mod1 : Alt_L Alt_R
Mod2 : Num_Lock
Mod3 : Meta_L
Mod4 : Meta_R
Mod5 : Ctrl_R
As you can see, Ctrl_R is removed from the Ctrl modifier ( I don't use right Ctrl anyway ), and it's assigned to Mod5 ( I also don't need Scroll_Lock ). Also, Meta_L is assigned to Mod3 and Meta_R to Mod4. ( On my keyboard, Meta_L is that key with the strange logo from Redmond on the left side, Meta_R is the same on the right ).
Now, Mod3 is assigned to Meta modifier, Mod4 is assigned to Super modifier and Mod5 to Hyper. This setting means that left Win key will act like Meta modifier, right Win key will be Super modifier, and right Control will be Hyper. All other modifier keys will work like before.
If all combo boxes list only Shift, Ctrl and Alt modifiers, you may use the Ctrl_R trick as described above. If you e.g. have the left and right Win keys on your keyboard ( 104 keys keyboard ), your X server is probably just not configured properly to recognize those keys. First check your keyboard settings in your X server configuration file ( e.g. /etc/X11/XF86Config ), and if that doesn't help, you'll need their keycodes, e.g. left Win key is 115, right one is 116, and the Menu key is 117. In your autostart folder, put a new file containing this ( don't forget to set it the executable flag. ) :
#! /bin/sh
xmodmap -e "keycode 115 = Meta_L"
xmodmap -e "keycode 116 = Meta_R"
xmodmap -e "keycode 117 = Menu"