Hi Paul,

You mentioned that it [the ugly fonts for Coot] may be a GTK thing and I just found the
following web page 
http://www.linuxcompatible.org/thread27498-1.html 
which explained how to change the default font for gtk-1 and  gtk-2.0 apps. 
Coot seems to be a gtk-1 app so all I had to do was the following:

1. copy /etc/gtk/gtkrc.utf-8 to ~/.gtkrc
2. edit the fontset line so that the first line reads
fontset = "adobe-helvetica-medium-r-normal--12-*-*-*-*-*-*-*,\

and start coot.

Martin