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%20Mole...> 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