All algorithms
Refinement
Stage
3
of 8
Included on all plans
CTF Refinement
Per-particle defocus, astigmatism, beam tilt, aberrations and anisotropic magnification refined in one job.
5 in 1
Optical parameters fitted in a single job
3x faster
Than RELION's CTF refinement
What it does
CTF Refinement fits defocus on a per-particle level, and corrects for astigmatism, beam tilt and magnification anisotropy, as well as higher order symmetrical and asymmetrical aberrations.
How it works
With a 3D map, each particle can be compared with a projection of the map at its refined orientation, and the optical parameters adjusted until the two agree. Because this uses phase as well as amplitude, it measures defocus per particle and is more precise than fitting a power spectrum. It also captures beam tilt and other odd-order aberrations, which shift only phases and so never show up in a power spectrum.
The parameters are correlated and improve as the map does, so the better the input, the more accurate the corrections.
In CryoCloud's published automated analysis of the gastric proton pump, a CTF refinement routine run on the same particle stack took the map from 2.6 to 2.4 Å.
Example outputs from CryoCloud CTF refinement showing change in per-particle defocus as well as changes to estimated astigmatism.
Where it sits
CTF Refinement is added downstream of 3D refinement. It is often followed by CryoCloud Polishing, which corrects per-particle motion. The two together, along with a final 3D refinement job are frequently the last steps employed to get the best resolution possible from the data available.
CryoCloud workflows can append a cycle of CTF refinement, polishing and refinement to an existing processing branch so that individual jobs do not have to be added by hand.
At a glance
Stage
Refinement
Runs
After 3D refinement
Hardware
Cloud compute
Inputs
Refined particles and a map
Outputs
Refined optical parameters
Defocus, astigmatism, beam tilt, aberrations and anisotropic magnification, ready for the next refinement round.
Replaces
RELION's CTF Refinement
Availability
Included
Take a good map to the resolution its data supports.
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