Table 2.
Initial parameters for 2D classification and 3D refinement
| 2D classification | 3D initial model | |
|---|---|---|
| Input particle and box pixel size | Input extracted particles from reference picking, 180 pix (bin 4) | Input selected 2D class particles, 180 pix (bin 4) |
| Reference map and symmetry | -- | Reference-free, C1 symmetry |
| Do CTF-correction | Yes | Yes |
| Number of classes | 50 | 1 |
| Regularization Parameter T | 2 | -- |
| Number of iterations | 25 | 25 (Initial); 100 (In-between); 25 (Final) |
| Mask diameter (Å) | 700 | -- |
| Sampling | Yes | -- |
| Running | 3 MPI 4-16 threads | 3 MPI 4-16 threads |
| Initial angular sampling (degrees) | -- | 15 |
| 3D classification | 3D auto-refine | |
| Input particle and box pixel size | Input particles from 3D initial model, 180 pix (bin 4) | Input selected 3D class particles, 180 pix (bin 4) |
| Reference map and symmetry | Input 3D initial model, low-pass filter to 60 Å and apply I3 or I4 symmetry | Input map from selected 3D class, low-pass filter to 60 Å and apply the same symmetry (I3 or I4) |
| Do CTF-correction | Yes | Yes |
| Number of classes | 4 | -- |
| Regularization Parameter T | 4 | -- |
| Number of iterations | 25 | -- |
| Mask diameter (Å) | 800 | 800 |
| Sampling | Yes | -- |
| Running | 3 MPI 4-16 threads | 3 MPI 4-16 threads |
| Initial angular sampling (degrees) | 7.5 | 7.5 (Initial), 1.8 (local search) |