[Chimera-users] General question about Chimera

[Elaine Meng]

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:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets>

... ligand and ions classification here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats>

... 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.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules>
I hope this helps,
Elaine
-----
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