# Parameters marked with (*) are optional
# All parameters that can be defined in a range ([min_value, max_value]) can also be
# defined as a single value (e.g., offset_x_in_angstroms: 0.0)

number_of_images: 20000
batch_size_for_generation: 1000 # images generated in parallel
images_per_file: 5000

data_sign: dark-on-light # Relion convention, dark particles on a light background
box_size: 128
pixel_size: 2.0

offset_x_in_angstroms:
  - min_value
  - max_value
offset_y_in_angstroms:
  - min_value
  - max_value

amplitude_contrast_ratio: 0.1
phase_shift: 0.0
spherical_aberration_in_mm: 2.7
voltage_in_kilovolts: 300.0

ctf_scale_factor: 1.0
astigmatism_angle_in_degrees:
  - min_value
  - max_value
astigmatism_in_angstroms: [min, max]
defocus_in_angstroms:
  - min_value
  - max_value
envelope_b_factor:
  - min_value
  - max_value

# Noise is added by normalizing the variance of the signal
# the following sets the region in the image used to compute the variance
# We recommend half the box size (can vary with pixel sizes and range of offset)
mask_radius: 64
mask_rolloff_width: 1.0 # smooths the edge of the mask
noise_snr:
  - min_value
  - max_value

atomic_models_params:
  atom_selection: not element H
  atomic_models_probabilities:
  - 0.7
  - 0.3
  loads_b_factors: true
  path_to_atomic_models: # use of wildcard is permited, e.g., `path/to/atomic_models/initial_model_*.pdb`
    - path/to/atomic_models/initial_model_0.pdb
    - path/to/atomic_models/initial_model_1.pdb
    - path/to/atomic_models/initial_model_2.pdb
    - ...
overwrite: true

path_to_relion_project: output/directory/for/mrcs/files/
path_to_starfile: path/to/starfile.star


rng_seed: 0 # seed for the noise and parameter generation