Query about NU-refine implementation

3D Refinement
1

Hi,

Is the NU-regularization in NU-refine carried out at every voxel in the box (with a sliding window controlled by the adaptive window factor)? Or just at voxels within a mask? And if the latter, which mask is used - mask_refine or mask_fsc?

The reason I ask is that in high resolution NU-refine jobs, we see a certain (relatively minor!) degree of “ringing” artifacts around strong protein features, even when dynamic masking is disabled.

Consequently I’m wondering if this is due to some other mask being used for NU regularization, or possibly due to the order of the Butterworth filter used for smoothing (I don’t think it’s this as reducing the order doesn’t seem to make a big difference)…?

Cheers
Oli

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2

Hey @olibclarke!

We apply the regularization to all the voxels inside the box. The static / dynamic mask is applied to the map prior to alignment, but the non-uniform regularization sees the entire reconstructed box (post alignment). We’ve found that the NU regularization does a good job of accounting for the solvent, so a mask isn’t necessary.

Could you post a screenshot of these ringing artifacts?

Thanks!
Valentin

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3

DMed it to you, thanks Valentin! And thanks for the details re implementation, very helpful!

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