| 0 |
Import |
— |
0–7, 10 |
Import/
|
Import files into the pipeline |
| 1 |
Motion correction |
0 |
0, 1, 13 |
MotionCorr/
|
Wraps to external motion-correction programs |
| 2 |
CtfFind |
1 |
1 |
CtfFind/
|
Wraps to external CTF estimation programs |
| 3 |
Manual picking |
1 |
1, 2 |
ManualPick/
|
Manual picking of particles |
| 4 |
Auto-picking |
1, 5 |
2 |
AutoPick/
|
Automated picking of particles |
| 5 |
Particle extraction |
1–3 |
3 |
Extract/
|
Extraction of particle boxes from the micrographs |
| 6 |
Particle sorting |
3, 5, 8 |
3 |
Sort/
|
Sort particles based on statistics in differences from reference images |
| 7 |
Subset selection |
1–3, 8 |
1, 3, 5 |
Select/
|
Select classes or subsets from lists of micrographs or particles |
| 8 |
2D classification |
3, 9 |
3, 8, 9 |
Class2D/
|
Reference-free two-dimensional class averaging |
| 9 |
3D classification |
3, 6, 7, 9 |
3, 6, 8, 9 |
Class3D/
|
Unsupervised three-dimensional classification |
| 10 |
3D auto-refine |
3, 6, 7, 9 |
3, 6, 8–10 |
Refine3D/
|
Gold-standard three-dimensional auto-refinement |
| 11 |
Particle polishing |
0, 7 |
3, 11, 13 |
Polish/
|
Per-particle motion correction and radiation-damage weighting |
| 12 |
Mask creation |
6 |
7 |
MaskCreate/
|
Generate mask from binarized map |
| 13 |
Join STAR files |
0, 1, 3 |
0, 1, 3 |
JoinStar/
|
Join sets of particles, micrographs or movies |
| 14 |
Particle subtraction |
3, 6, 7 |
3 |
Subtract/
|
Subtract projections of (masked) maps from experimental particles |
| 15 |
Post-processing |
10, 7 |
11, 13 |
PostProcess/
|
Solvent-corrected FSC calculation and map sharpening |
| 16 |
Local resolution |
7, 10 |
12 |
ResMap/
|
Local resolution estimation |
| 17 |
Movie refinement |
4, 9 |
4, 6, 8, 10, 13 |
MovieRefine/
|
Extract particles from movies and align against three-dimensional reference |
