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I've remapped a certain key (` to w) with this way:

xmodmap -e "keycode 49 = w"

I use Greek language, not only English and I change between languages with ALT+SHIFT. When I turn the keyboard layout to Greek it should output a greek character that is assigned to w key at greek keyboards (the character ς). It continues to output w when I turn the keyboard to Greek. The name that is given to this greek character (when I press w/ς key after xev at the terminal with the language turned to Greek) is Greek_finalsmallsigma

Temporarily I did the following in order to output the greek character by pressing Shift

xmodmap -e "keycode 49 = w Greek_finalsmallsigma"

Is there a way to change the output of that key when I change between Greek and English with ALT+SHIFT ?

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Open a terminal (Ctrl+Alt+T), or press Alt+F2 for a run-command textbox. Type:

gksu gedit /usr/share/X11/xkb/symbols/gr

Find the line starting with:

key <AD02>

and replace it with:

key <AD02> { [ Greek_finalsmallsigma,    Greek_SIGMA ] }; // ς Σ

Then save the file and restart your computer.

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