Dynamic mask z-clip fraction override?

Helical Processing
1

Hi,

I noticed when trying to set the z-clip fraction to relatively small in helical refinement that it is automatically increased, with the text below:

Increasing dynamic mask z-clip fraction to 0.507, to cover at least 12 helical rises

Is it possible to override this behavior for flexible filaments? Do I need to make a custom mask?

Thank you,

Axel

2

Hey @abrilot ,

When using a dynamic mask, the value CryoSPARC uses for the z-clip fraction depends on the helical symmetry order enforced. Based on the helical symmetry order, the z-clip fraction is set to be greater or equal to the helical rise multiplied by the helical symmetry order. This was done mainly so that the dynamic mask doesn’t clip too much of the density away, as global pose search is known to find worse results as the masks decrease in size.

For especially flexible filaments, it is possible to create a Static Mask via Volume Tools that has a smaller z-clip fraction, and run Helical Refinement with this mask. However, a better approach would be to run the following in sequence:

  1. A consensus Helical Refinement with normal masking, then
  2. Symmetry expansion on your filament particles after Step 1, using the known helical parameters, then
  3. Local Refinement on these particles, with the aforementioned Static Mask covering the central region of interest.

It’s recommended to use local refinement for this purpose as it is specifically tuned to handle the case of smaller masks + small pose changes.

Michael

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