Asymmetric refinement without masking



I would like to refine an entire (unmasked) virus in asymmetric mode. If I switch from icosahedral (I) to asymmetric (i), and do not specify any masks, will the structure change from its initial reference?

I'm unclear how exactly the reconstruction uses symmetry-related orientations to bring out asymmetric features. It seems like all 60 orientations are being used for the reconstruction. Without a mask, are the orientations for a single particle evaluated against each other to determine which orientation has a higher likelihood?


Without a mask it is unlikely that the reconstruction will change much because all 60 orientations will be close to the orientations imposed by icosahedral symmetry. You will have to use a mask that includes just the feature you are trying to align or classify. Keep in mind that alignment on a small feature in the capsid will probably fail. The best masking strategy will depend on what you want to achieve.

In reply to by niko

Ok thanks! If instead of switching to sym i, I switch to sym C1 mode 3, is there anything gained from the initial refinement in sym I? Is there a more efficient way to do symmetry relaxation?