Masks¶
A real-space mask is important to boost SNR by focusing the analysis on the region of interest.
Solvent mask¶
Most consensus reconstruction software outputs a solvent mask. Use it directly:
Warning
Make sure the mask is not too tight. Use --mask-dilate-iter to expand it if needed.
Auto-generated masks¶
If you don't have a mask:
| Option | Description |
|---|---|
--mask=from_halfmaps |
Estimate mask from the mean reconstruction (averages half-maps, low-pass filters, Otsu thresholds, cleans up, and softens) |
--mask=sphere |
Use a loose spherical mask |
--mask=none |
No mask (not recommended) |
A good approach is to first run with --mask=sphere, inspect the variance map to see which regions have heterogeneity, then create a focused mask around those regions.
Focus mask¶
A focus mask restricts the heterogeneity analysis to a specific region of the molecule. This is useful when you're interested in a particular domain or binding site.
If you only have a focus mask:
Creating a focus mask¶
You can create a focus mask in UCSF Chimera or ChimeraX:
- Open your consensus map
- Select the region of interest
- Create a mask around that region
- Save as
.mrc
See cryoSPARC's guide on mask generation for step-by-step instructions.
GUI mask selection
In the web GUI, you can browse and select mask files when creating a pipeline job — or choose from_halfmaps / sphere from a dropdown.
Mask dilation¶
To expand a mask by a few pixels:
The --mask-dilate-iter flag applies to both the solvent mask and the focus mask.