On Wed, Oct 29, 2008 at 11:39 AM, Thomas S. Leyh, Ph. D. <leyh@aecom.yu.edu> wrote:
    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?

I think you want "hide nonbonded".

I have a related question: is there a way (or could there be) to control the default appearance of molecules upon loading?  Personally, when I use PyMOL I almost always want to look at cartoons, without nonbonded atoms.  Something as simple as a few new settings that I could throw in ~/.pymolrc would be fine.