Here is the xmodmap code in my Thinkpad T41p for swapping CTRL and ALT keys.
These keycodes are system-specific. Use `xev` to find out the keycodes in your system before applying this `xmodmap` script.
!
! This is an `xmodmap' input file for
! PC 105 key, wide Delete, tall Enter (XFree86; US) keyboards.
! Automatically generated on Sat Nov 22 23:28:24 2008 by xxxxx with
! XKeyCaps 2.47; Copyright (c) 1991-1999 Jamie Zawinski; 2005-2006 Christoph Berg.
! http://www.jwz.org/xkeycaps/
!
! This file presupposes that the keyboard is in the default state, and
! may malfunction if it is not.
!
remove Lock = Caps_Lock
remove Control = Control_L Control_R
remove Mod1 = Alt_L Alt_R
remove Mod4 = Meta_L Meta_R
remove Mod5 = Scroll_Lock
keycode 0x42 = Alt_L Meta_L
keycode 0x25 = Alt_L Meta_L
keycode 0x40 = Control_L
keycode 0x71 = Control_R
keycode 0x6D = Alt_R Meta_R
add Control = Control_L Control_R
add Mod1 = Alt_R Alt_L 0x009C Alt_L Alt_R Alt_L Alt_L
add Mod4 = 0x007F 0x0080
add Mod5 = Mode_switch ISO_Level3_Shift
!
! For Mouse Swap.
!# pointer = 3 2 1 4 5
Check more tips at , http://steve.yegge.googlepages.com/effective-emacs

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