[Chimera-users] measure symmetry

Tom Goddard goddard at sonic.net
Wed Oct 8 11:34:44 PDT 2014

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.


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

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