You are right that the EMDB 1220 virus capsid has none of the standard icosahedral orientations. It is approximately 3-fold axis along z, and 2-fold axis along x (Chimera orientation 2n3r) but it is maybe 5 degrees off from that. If this capsid was refined with C1 symmetry then there is no reason for it to have a standard orientation. It will be difficult to compute the icosahedral symmetry matrices. I suggest you talk to the author of that map Gabe Lander who has a lab at Scripps, right where you are located.

On Oct 8, 2014, at 2:07 PM, Reginald McNulty wrote:

Thanks. It works.
I’m trying to do the same thing now for a virus with a tail. It was refined with C1 symmetry. The icosahedral symmetry in the capsid is evident. But I can’t get the icosahedal surface to match the symmetry exactly. Can you take a look at this map: emd_1220.map?
Reggie
On Oct 8, 2014, at 11:34 AM, Tom Goddard wrote:

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

<2xyz.jpg>

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