On Wed, Oct 29, 2008 at 11:39 AM, Thomas S. Leyh, Ph. D. <email@example.com> 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.