Hi C.J., I assume you are looking at a density map. In that case... There is a Volume Eraser tool (under Tools... Volume Data) that allows you to position a sphere interactively and then erase the density inside or outside the sphere. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser...> However, it might be hard to position the sphere interactively. A similar approach would be to use the "shape" command to place a sphere, and in that case you can enter the center coordinates, and then the "mask" command to erase the density outside that sphere. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> There is also the "vop" command with which you could chop out an octant: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.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 Oct 24, 2010, at 9:50 AM, jh wrote:

Dear all, I want to mask area outside certain surface and to visualize the inner capsid of a virus by Chimera. Anyone would be kind to help me with that? C.J.