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3D classification
Stage
2
of 8
Included on all plans
AutoClass3D
3D classes selected against a reference, or on resolution when no reference is given, so heterogeneity is separated without a person deciding which map looks right.
Two criteria
Correlation to a reference, or resolution
Masks follow
Masks are automatically generated for the selected volume
What it does
A particle stack is often highly heterogeneous. It holds different conformations, different compositions, particles that are damaged, as well as complete junk. Reconstructing all of them into one map averages those states together and blurs the regions that differ, which are often the interesting ones.
3D classification separates the particle stack on these differences so each state can be refined on its own. AutoClass3D automatically selects the class or classes that will be taken forward for downstream processing e.g. 3D refinmement or further rounds of classification.
How it works
Automatic selection of 3D classes happens one of two ways. Given a reference, classes are scored by cross-correlation against it (a Pearson correlation and a Fourier shell correlation). Accepted classes are marked in the results page.
Where no reference is provided, or where the preceding job sorted particles without alignment, the criterion becomes resolution and the highest-resolution class is taken forward.
Masks are generated automatically for the volumes AutoClass3D selects, so the next stage does not wait on a manual masking step.
Autoclass3D results page. One of three classes is selected based on the FSC and Pearson correlation thresholds.
Where it sits
AutoClass3D comes after 3D classification and before refinement. It decides which 3D classes and therefore which particles to take forwards.
At a glance
Stage
3D classification
Runs
Following 3D classification
Hardware
GPU
Inputs
Data and Model star files from 3D classification
Outputs
Selected 3D class and corresponding particles
Masks are generated automatically for the selected volumes.
Replaces
Availability
Included
Separate the states in your data without choosing by eye.
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