All algorithms
Masking
Stage
3
of 8
Included on all plans
AutoMask Job
Shape masks generated from the map itself, with dilation optimised for accurate resolution estimates instead of tuned by hand.
Shape mask
Follows the density, not a sphere
Optimised dilation
Tuned for more accurate resolution estimates
What it does
Most late-stage cryo-EM steps need a mask: a definition of which part of the box is the molecule and which is solvent. Masks decide what resolution estimates are measured over and what sharpening acts on.
Building one by hand means choosing a threshold, a radius and a soft edge, and those choices change the numbers that come out. AutoMask generates a shape mask from the map itself, and CryoCloud's refinement jobs use one by default rather than a sphere.
How it works
The map is separated from solvent and lowpass filtered. The boundary is extended such that the molecule is fully enclosed, and the edge is softened, because a sharp edge introduces artefacts in Fourier space.
Setting the correct dilation and soft edge is important. Too tight cuts into the molecule and inflates the estimate; too loose includes excess noisy solvent. CryoCloud can optimise that dilation automatically for more accurate resolution estimates.
Shape mask output from the AutoMask job. The mask is show in transparent green and is overlaid on the input volume.
Where it sits
AutoMask is used wherever a mask is needed: refinement, resolution estimation and post-processing.
When you need a mask for one region rather than the whole molecule, Interactive Masking is the tool for that.
At a glance
Stage
Masking
Runs
Throughout workflow
Hardware
GPU
Inputs
A 3D map
Outputs
A soft-edged shape mask
Used for refinement, resolution estimation and post-processing, with the mask shown over the volume in the results.
Replaces
Availability
Included
Put this algorithm to work
See the full system around the workflow step, then choose the right way to get started.
TECHNOLOGY OVERVIEW
Explore all algorithms
Browse the complete analysis workflow, from pre-processing to refinement.
View algorithm overview
PLAN WITH CONFIDENCE
See what’s included
Compare plans, compute, and storage with transparent costs for every workflow.
Explore pricing
SEE YOUR DATA FLOW
Book a guided demo
Talk through your data, workflows, and deployment needs with a CryoCloud specialist.
Book a demo