# What should be done? ctf window isac viper refine sort
#what_to_do = unblur,ctf,window,isac,viper,refine,sort,local
#what_to_do = ctf,window,isac,viper,refine,sort,local
#what_to_do = window,isac,viper,refine,sort,local
#what_to_do = isac,viper,refine,sort,local
#what_to_do = viper,refine,sort,local
what_to_do = refine,sort,local
#what_to_do = sort,local
#what_to_do = local
#what_to_do = unblur,ctf

# Project settings
output_path = XXX_TEST_FOLDER_XXX
output_name = XXX_TEST_FOLDER_NAME_XXX

# Project specific changes
movie_path = Movies/TcdA1-010*_frames.mrc
box_files_path = Precalculated-Results/Coordinates/corrsum_dose_filtered-TcdA1-*_frames_sum.box
mtf_file = FalconIImtf.txt
#uncorrected_sums_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_UNBLUR/corrsum/TcdA1-*_frames_sum.mrc
#corrected_sums_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_UNBLUR/corrsum_dose_filtered/TcdA1-*_frames_sum.mrc
uncorrected_sums_path = Precalculated-Results/CorrectedSums/corrsum/TcdA1-*_frames_sum.mrc
corrected_sums_path = Precalculated-Results/CorrectedSums/corrsum_dose_filtered/TcdA1-*_frames_sum.mrc

# Both is necessary
box_size = 352
box_size_binned = 352
# Use the original ones
particle_radius = 145
pixel_size = 1.14
symmetry = C5
# Unblur settings
unblur_path = /work/software/unblur/bin/unblur_openmp_7_17_15.exe
summovie_path = /work/software/summovie/bin/sum_movie_openmp_7_17_15.exe
nr_of_frames = 24
exposure_per_frame = 2.5
# CTF settings
cs_value = 0.01
f_start = 0.0285
f_stop = 0.285
ctf_window_size = 512
# ISAC settings
isac_subsets = 1
img_per_group = 100
# Initial Settings
n_v_runs = 9
mask_init_thresh = 13
mask_init_ndilation = 9
mask_init_kernel = 11
# Refine settings
memory_per_node_ref = 64
ini_res = 18
mask_sharp_thresh = 0.02
b_sharp_start = 3
b_sharp_stop = 10
# Refine continue
memory_per_node_ref_continue = 64
# SORT3D settings
var_fl = 0.056
var_aa = 0.1
memory_per_node_sort = 64
minimum_grp_size = 500
img_per_group_sort = 4500
memory_per_node_sub = 64
mask_sharp_thresh_sort = 0.02
b_sharp_start_sort = 10
b_sharp_stop_sort = 3
low_pass_filt_freq = -1
# local res settings
fourier_step = 2
overall_res = 0.329

# Output paths
output_unblur_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_UNBLUR
ctf_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_CTF
particles_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_PARTICLES
isac_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_ISAC
initial_3d_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_INITIAL_3D
initial_3d_post_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_INITIAL_3D_POST
refine_3d_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_REFINE_3D
refine_3d_sharpening_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_REFINE_3D_SHARPENING
sort_3d_preprocess_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_SORT_3D_PREPROCESSING
sort_3d_estimation_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_SORT_3D_ESTIMATION
sort_3d_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_SORT_3D
sort_3d_subset_ref_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_SORT_3D_SUBSET_REF
sort_3d_sharp_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_SORT_3D_SHARPENING
local_res_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_LOCAL_RES
local_filt_path = XXX_TEST_FOLDER_XXX/XXX_TEST_FOLDER_NAME_XXX_LOCAL_FILT