Post symmetry expansion and local refinement

Local Refinement
1

Hi folks,

After symmetry expansion (C7) and local refinement with mask on just single subunit I have an excellent single subunit map. How do I apply the symmetry (C7) back to the map to make it complete? Right now I just have a single subunit map and I want it to be a complete C7 ring.

Any thoughts or ideas are appreciated.

Thank you

Prash

2

Align seven copies with your overall C7 reconstruction, then combine (vop maximum in Chimera) and apply C7 symmetry (e.g. using relion_image_handler)?

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3

This worked!
Thank you @olibclarke, you are a genius!

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4

Hi Oli,

Thanks for the explanation ā€” this is very helpful. I just wanted to ask one clarifying question to make sure Iā€™m understanding this correctly.

If Iā€™m not mistaken, in CryoSPARC workflows involving symmetry expansion followed by local refinement on a single subunit of a symmetric structure (for example, a vertex of an icosahedral virus), CryoSPARC does not automatically produce a symmetrized map from the local refinement. Instead, the local refinement generates a high-quality map of one asymmetric subunit using all symmetry-related copies (e.g., all 12 vertices across all virion images), and a full symmetric map is then reconstructed by replicating and assembling this refined subunit according to the symmetry.

This point has been troubling me for a while, and I just want to confirm whether this interpretation is correct for CryoSPARC.

Thanks again for your time and insight.

Best,
Wenxuan

5

What you describe is technically correct. But I question whether making a composite map is the correct thing to do.

The very reason you need to classify asymmetric units and run signal subtraction and local refinement on each class separately is because there are local features deviating from the overall symmetry: different conformations of the subunits, different interactions at the interfaces between neighboring subunits, different relative orientations between neighboring subunits, or some combination of all these. If there were no local deviations from perfect symmetry, then the global refinement with symmetry enforced would already have produced that perfectly symmetric map that you are trying to make as a composite map using multiple copies of the locally refined map.

So, this composite map represents an ideal particle with perfect symmetry that in fact does not exist in the dataset (otherwise the global refinement with symmetry would have produced its reconstruction). Does it make sense to generate this map? I think not, because it does not faithfully represent the underlying data.

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