[Chimera-users] changing ion appearance

Elaine Meng meng at cgl.ucsf.edu
Sat Nov 22 19:15:37 PST 2008

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.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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