Synthetic Dataset Creation¶

This method uses projections of a 3D model in order to create a synthetic dataset. Although it can be modified according to the options specified, the scheme consists of 12 basic steps, as shown and summarized below:

1. a model is chosen from which projectinos are created
2. the model is projected either in an even distribution or with axial preference
3. the projections are randomly rotated in the XY plane
4. the projections are randomly shifted in the XY plane
5. white Gaussian noise is added
6. a contrast transfer function is added according to the specified defocus parameter and the spherical aberration constant of the microscope
7. an envelope function is added according to an experimentally determined decay function from 3000 real micrographs (see Voss, N, Lyumkis, D. et al, JSB (2010) 169, 3, 389-98).
8. a second level of Gaussian noise is added, usually to bring the signal-to-noise ratio down to ~0.05, consistent with real ice data (see Baxter, WT, et al, JSB (2009) 166, 2, 126-32).
9. (optional) the CTF is estimated by ACE2 and corrected
10. (optional) the particle is band-pass filtered
11. final particle of 50S ribosomal subunit with a SNR of 0.05
12. particle is added to a growing stack of synthetic particles