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Asymmetric refinement without masking

3 replies [Last post]
mtherkel
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Joined: 19 Apr 2015

Hi,

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?

Thanks,
Matt

niko
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Joined: 5 May 2009
Without a mask it is unlikely

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.

mtherkel
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Joined: 19 Apr 2015
Ok thanks! If instead of

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?

niko
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Joined: 5 May 2009
You could always restart your

You could always restart your refinement in C1. This would then make sure that symmetry is never imposed.