Final 3D map slightly asymmetric

[Carsten Sachse]

Dear Carsten,
 
I have one doubt. In the final 3D map, despite the imposed symmetry, there are clear differences between subunits. My experience with Cn symmetry is that there are differences but rather small. I recall authors working with icosahedral viruses calculating averages between capsomers from the 3D maps.
 
Should we isolate subunits and make a 3D average to get the consensus structure? Should we use only a subset of them (something close to the asymmetric unit?).
 
Best.    

Dear Mikel,

This is expected because for high and maximum resolution refinement the final map is not symmetrized in 3D but only during the reconstruction. All asymmetric units have been averaged from the images but because of the reconstruction algorithm and the noise you will have slight asymmetries remaining in the volume. You can symmetrize and beautify your map using SEGREFINE3DINSPECT using the 'long helix' option to generate a volume for inspection of the desired length.

Best wishes,

Carsten