Hi CE, Sure, you can do it with the "transparency" command (in Chimera 1.7 and newer), for example: transparency 65,a sel ... to make the selected atoms 65% transparent. For details and options, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#transparency> The "sel" means the selected atoms, but alternatively, you can specify the atoms directly instead of having to select them first: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> 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 Apr 22, 2014, at 5:27 PM, Chinaza Egbuta wrote:

Hi, Is there a way to change the transparency of selected atoms in a model? I am trying to visualize what is behind the plane of my model without using the surface capping function. Thanks! CE

Chinaza Egbuta Ph.D. Candidate Department of Pharmacology & SUNY Upstate Cancer Research Institute SUNY Upstate Medical University Syracuse, NY 13210