Hi Sc Ke, There is more than one way. Say you have already selected the single atom. Then, (A) to put a marker (essentially a fake atom) at that position, command “measure center”, for example: measure center sel mark true radius 4.0 color pink model #8 transparency 50 #8 see manual for command options <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html> (B) to put a spherical surface model at that position, command “shape sphere”, for example: shape sphere radius 8.5 center sel color orange modelid #8 transparency 60 #8 see command options <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#sphere> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Mar 4, 2020, at 2:40 AM, Ke Shyue-Chu <ke@gms.ndhu.edu.tw> wrote:

Hi, I would like to know how to create a sphere of certain radius around a selected atom, for visualization purpose. Thank you. Sc Ke Professor Department of Physics National Dong Hua University Hualien, Taiwan