[Chimera-users] Map Orientation for Symmetry Plug-in

Albion Baucom baucom at msg.ucsf.edu
Mon Feb 5 16:43:54 PST 2007

I am using the Symmetric Molecule Copies plug-in with Chimera.

I am wondering if there is a preferred way to orient an EM volume so  
that it is centered around the z-axis at the origin. From my  
experience with this plug-in, symmetry related molecules are  
generated around z-axis at the origin of the viewing area. I am  
finding that my maps tend to be close, but not exactly oriented  
around the z-axis for a helical volume. Molecules fit into a portion  
of the map then tend to have slightly askew symmetry mates relative  
to the volume (presumably because the z-axis of the map is not  
exactly oriented along the origin of the symmetry z-axis).

After playing around with various map tools (MAPMAN, Priism), I am  
still not satisfied with my orientation protocol and wonder if anyone  
can suggest a tried and true method for this.



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