Appion

h1. 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:

!http://emg.nysbc.org/attachments/294/Supplementary_Figure_5_-_Synthetic_dataset_creation.png!

# a model is chosen from which projectinos are created

# the model is projected either in an even distribution or with axial preference

# the projections are randomly rotated in the XY plane

# the projections are randomly shifted in the XY plane

# white Gaussian noise is added

# a contrast transfer function is added according to the specified defocus parameter and the spherical aberration constant of the microscope

# 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).

# 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).

# (optional) the CTF is estimated by ACE2 and corrected

# (optional) the particle is band-pass filtered

# final particle of 50S ribosomal subunit with a SNR of 0.05

# particle is added to a growing stack of synthetic particles

!http://emg.nysbc.org/attachments/277/Picture_81.png!