[Chimera-users] General question about Chimera

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 6 09:24:35 PST 2014

Hi Lili,
The default "smart initial display" uses rules similar to the ribbons preset, including showing residues within 3.6 A of residues classified as ligand or metal ions.  The ribbons preset (e.g. menu: Preset... Interactive 1 (ribbons)) is described in more detail here:

... ligand and ions classification here:

... and the smart initial display is a setting in the New Molecules category of Preferences.  You can change various preferences in that category if you want a different initial appearance.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 5, 2014, at 11:42 PM, Lili Peng wrote:

> Hi,
> When I load a structure of a protein into Chimera, the structure is automatically rendered in ribbon mode, with select atoms being rendered in stick mode.  I am curious as to why certain atoms are rendered as sticks, and other are not.  What is the selection criteria?
> Thank you,
> Lili

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