Can I get urxvt to recognize xmodmap configuration?

Question

i switch from an apple-style keyboard at home to a microsoft-style keyboard at work. the primary difference in these keyboards is that the super key and the alt key are transposed. i've used xmodmap to fix this; emacs recognizes the change using X11, but not under xterm or urxvt! is there a way to make urxvt or xterm recognize the xmodmap change?

for reference, here is my xmodmap configuration:

remove Lock = Caps_Lock
keysym Caps_Lock = Hyper_L
remove Mod4 = Hyper_L
clear Mod3
add Mod3 = Hyper_L

!swap alt and win on the left side...i use a mac keyboard at home.
remove Mod1 = Alt_L
remove Mod4 = Super_L
add Mod1 = Super_L
add Mod4 = Alt_L