Advice for subtraction masks?

Any one have advice about mask parameters for particle subtraction and local refinement?

I’m getting artifactual resolution numbers at the interface between what’s kept and what’s subtracted. Image of particularly bad example with resulting map colored by resolution attached. Actual map is 5-8 Å. But the interface region reports << 5, something like 1-Å resolution (and is thus totally red, since I’ve set red = 5).

My workflow is only a slight variation of the tutorial:

  1. Rather than make masks in Chimera, I segment the map in Chimera and save the selected regions to MRC file, noting the center location and my desired threshold.
  2. Then I make a refinement mask is cryoSPARC, with above threshold value, dilation and soft-padding values variable. This is what I want to keep.
  3. Then I make the subtraction mask in cryoSPARC from the refinement mask using the invert mask feature of the volume tools. Here variables include threshold, as well as dilation and soft-padding.
  4. Then particle subtraction and local refinement (with center from step 1).

Pictured example used settings from the tutorial, low threshold value, 5 pix dilation, 0 soft padding.

I’ve made various attempts and nothing seems to get rid if altogether, although some combinations are better and some are worse.

It’s the interplay between the refinement mask and the subtraction mask I’m unsure about.


If it matters, using version: v2.14.2

Hi @rj.edwards,

Have you tried changing the dynamic masking params for this, as you mentioned here: