When I tried it out, ioquake3 installed /home/user//baseq3 ant NOT /home/user/MyDocs/baseq3.

First, I moved everying (including the pk3 files) to /home/user/.q3a/baseq3/, but Quake 3 would not start. When I moved the files back to /home/user//baseq3 Quake 3 started up and everything worked fine.