5x faster
In benchmark runs compared to relion
Written from scratch
Our own engine, not a wrapped or patched RELION.
What it does
3D refinement estimates the orientation and in-plane shift of each particle image relative to a reference map, then reconstructs the map from the aligned images. It iterates until the resolution stops improving.
How it works
CC Refine follows the established Bayesian framework. Particles are split into two independent half-sets that are refined separately. Resolution is estimated from the Fourier shell correlation (FSC) between the two half-maps at the 0.143 threshold, which prevents overfitting from inflating the reported resolution.
As an option, Blush regularisation (Kimanius et al., Nat. Methods 2024) replaces the standard smoothness prior with a denoising network. This helps where the conventional prior limits alignment, typically for small particles, membrane proteins in micelles or nanodiscs, and flexible regions.
test
Where it sits
CC Refine runs after 3D classification, starting from a curated particle stack and an initial reference. It is followed by CTF refinement and Bayesian polishing, and it can be run again on the polished particles.
At a glance
Stage
Refinement
Runs
Following 3D classification
Hardware
GPU
Inputs
Particles
Outputs
3D map
Map & Particles star fie with statistics
Replaces
Refine3D (Relion)
Availability
Included
Push a finished map towards the resolution the data can support.
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