Hi Xinlei, It may be that you need to turn off the "cap high values at box faces" option, as described in this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002455.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 Feb 25, 2010, at 2:39 PM, Huang, Xinlei wrote:

Hi, Thank you for inventing the software, it rocks! By the way I have a question about viewing the 3D reconstruction image of a Virus like particle containing small nanoparticle cores. When I tried to increase the electron density in order to see the inside cores there always was a box showed up along with the nanoparticle. I want to know is there a way to remove the outside box? Here I attach an image to explain better what I mean. I appreciate you help.