Well first of all we need to know if its choppy because you have bad (low) fps or bad (high) ping when playing online. If you play campaign or instant action or use the 'create' menu it will be a local game against bots so in that case it just can be choppy because of fps.
You can also display those two values. Ping is displayed in the scoreboard (the lower the better, i'd say anything over 100 IS BAD) and the FPS can be enabled in the 'options/effects' menu. Its called 'Show FPS'.
That being said ati drivers for linux are really bad performance wise and from what the others say its not even a very good graphics card. To you can try to lower the effects in Nexuiz to get more FPS like its mentioned here:
http://forums.alientrap.local/viewtopic.php?t=90 (Section 'Nexuiz is too slow/fast')