Hi Reggie, I used the following Chimera commands to create an icosahedral cage for virus capsid 2xyz and density map for full capsid, image attached. Tom open 2xyz rainbow chain sym #0 surf true # Used Tools / Higher-Order Structure / Icosahedron Surface to figure out orientation is n25r (no sym on x, 2-fold on y, 5-fold on z, with extra rotation). shape icos radius 400 orient n25r lattice 2,1 color blue linewidth 5 molmap #0 10 sym i,n25r On Oct 8, 2014, at 10:40 AM, Reginald McNulty wrote:

Dear Tom,

I’ve imported a virus capsid shell pdb 2xyz to chimera. I want to measure the symmetry and make a cage based on that symmetry. Molmap seems to only produce a map of the asymmetric unit, not the entire capsid. Any thoughts? I’m currently following directions that are here: http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html

All the best, -Reggie

-- Reginald McNulty, Ph.D. Postdoctoral Research Associate The Scripps Research Institute Johnson Lab Department of Integrative Structural and Computational Biology 10550, N. Torrey Pines Road, MB-31 La Jolla, California 92037