To do this manually you want to create a file called .Xmodmap in your home directory. You could do this using a command from the terminal

~$ gedit ~/.Xmodmap

That will create the file and open it in gedit. Add the following lines to the file:

clear control

clear mod1

keycode 37 = Alt_L Meta_L

keycode 64 = Control_L

add control = Control_L Control_R

add mod1 = Alt_L Meta_L

Save the file and quit gedit. Next time you login the new keymappings will be active. To have the settings take immediate effect run the following command:

~$ xmodmap ~/.Xmodmap

There's a chance that the keycodes above are different on your computer. If the above doesn't work, try running the xev program from the command line. Xev will generate a new small window in the corner of your screen. If you start pressing keys on your keyboard you’ll get all the key mapping information for that key press.

~$ xev

For example if I press “q” when xev is running I get the following output:

KeyRelease event, serial 33, synthetic NO, window 0x4c00001,

root 0xb6, subw 0x0, time 9127480, (21,-17), root:(22,36),

state 0x0, keycode 24 (keysym 0x71, q), same_screen YES,

XLookupString gives 1 bytes: (71) "q"

XFilterEvent returns: False

keycode 24 is the information that we're after. Press your left Ctrl and left Alt buttons while running xev to get your own respective keycodes to confirm that they are the same as the ones used above.

Hope that helps.