Why do some of the maps of homogeneous refinement have lower quality than the 3d variability display?

3D Variability Analysis
1

Hi,

I performed 3d variability (mode:5) and 3dva display(cluster, cluster number 10).
Then, I carried out homogeneous refinement each of the clusters in the 3d variability display, and obtained some of the maps that have lower quality than the 3d variability display.
Why were they obtained?

Thank you.

2

Hi @rosetta66rose!
Thanks for your question about the difference in map quality between 3DVA cluster mode outputs and from subsequent homogeneous refinement.

We expect pose assignment to generally be more accurate with a larger (clean) particle stack due to the higher signal-to-noise ratio that this provides. Reconstructed maps from 3DVA Display use the poses from the input refinement that used all of the particles, and so those poses may provide a better quality map than if you take a relatively small particle set (such as a cluster) and re-estimate poses by global (Homogeneous or NU-) Refinement.

In some cases, Homogeneous Reconstruction without re-estimating poses (such as the 3DVA Display output volumes) is the best you can get for low population particle sets, but in other cases it maybe worth trying Local Refinement with a global mask, turning on Use pose/shift gaussian prior during alignment to restrict how far from the input poses the refinement can diverge.

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