On Nov 22, 2008, at 5:17 PM, Barry Lever wrote:

Elaine- a small question. I load up various ruthenium complexes as mol2. files into Chimera and invariably they appear as attached, with the central Ru atom as a huge ball, and the other atoms not appearing - how do I get rid of that huge ball or how do I make it much smaller ??

Hi Barry, By default, ions are initially shown in the sphere representation. Any atoms can be undisplayed or shown in a different representation (wire, stick, ball-and-stick). For example, you could select it with Ctrl-click and then use "Actions... Atoms/Bonds... hide" (or in the same menu, choose some other representation such as "stick") or use commands, for example: repr ions wire - or - ~display ions If you never want ions to be shown initially as spheres, you can change the Preferences (Favorites... Preferences, choose Category "New Molecules", change "monatomic ion style" to whatever you want, click "Save"). You might want to change additional settings in that panel, for example to show the other atoms/bonds with thicker lines or in a different representation. These preferences will apply to subsequently opened structures. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New% 20Molecules> Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html