you need to hide the 'nonbonded' representation of your ion, which shows up as a little coordinate system i.e.
hide nonbonded, chain I    #if your ion is in chain I
show spheres, chain I
set sphere_transparency=0.5, chain I
-----Original Message-----
From: Thomas S. Leyh, Ph. D. []
Sent: Wednesday, October 29, 2008 2:39 PM
Subject: [PyMOL] remove cartesian coordinate from w/in transparent metal ions

    Every once in a while, I try to show a metal ion as a tranparent sphere and inevetiably get stuck trying to make the tiny cartesian coordinate system that appears at the center of the sphere disappear so it doesn't "show through".  Suggestions?
Tom Leyh