subtom_maskcorrected_fsc

Calculates a “mask-corrected” Fourier Shell Correlation between two volumes and generates a final average as well as optionally ad-hoc B-factor sharpened maps.

This script is meant to run on a local workstation with access to an X server in the case when the user wants to display figures. I am unsure if both plotting options are disabled if the graphics display is still required, but if not it could be run remotely on the cluster, but it shouldn’t be necessary.

This EM-map analysis script uses just one MATLAB compiled scripts below:

subtom_maskcorrected_FSC

Options

Directories

scratch_dir: Absolute path to the folder with the input to be processed. Other paths are relative to this one.
mcr_cache_dir: Absolute path to MCR directory for the processing.
exec_dir: Directory for executables.

Variables

fsc_exec: Mask-corrected FSC executable.

File Options

ref_a_fn_prefix: Relative path and filename prefix of the first half-map.
ref_b_fn_prefix: Relative path and filename prefix of the second half-map.
iteration: The index of the reference to generate : input will be ref_{a,b}_fn_prefix_iteration.em (define as integer).
fsc_mask_fn: Relative path and name of the FSC mask.
filter_a_fn: Relative path and name of the Fourier filter volume for the first half-map. If not using the option do_reweight just leave this set to “”
filter_b_fn: Relative path and name of the Fourier filter volume for the second half-map. If not using the option do_reweight just leave this set to “”
output_fn_prefix: Relative path and prefix for the name of the output maps and figures.

FSC Options

pixelsize: Pixelsize of the half-maps in Angstroms.
nfold: Symmetry to applied the half-maps before calculating FSC (1 is no symmetry).
rand_threshold: The Fourier pixel at which phase-randomization begins is set automatically to the point where the unmasked FSC falls below this threshold.
plot_fsc: Plot the FSC curves - 1 = yes, 0 = no

Sharpening Options

do_sharpen: Set to 1 to sharpen map or 0 to skip and just calculate the FSC.
b_factor: B-Factor to be applied; must be negative or zero.
box_gaussian: To remove some of the edge-artifacts associated with map-sharpening the edges of the map can be smoothed with a gaussian. Set to 0 to not smooth the edges, otherwise it must be set to an odd number.
filter_mode: There are two mode used for low pass filtering. The first uses an FSC based threshold (mode 1), i.e. after FSC < 0.143, or a pixel-based resolution threhsold (mode 2).
filther_threshold: Set the threshold for the low pass filtering described above. Should be less than 1 for FSC based threshold (mode 1), and an integer value for the Fourier pixel-based threshold (mode 2).
plot_sharpen: Plot the sharpening curve - 1 = yes, 0 = no.

Reweighting Options

do_reweight: Set to 1 to apply the externally calculated Fourier weights filter_A_fn and filter_B_fn to each half-map to reweight the final output map.

Example

scratch_dir="${PWD}"

mcr_cache_dir="${scratch_dir}/mcr"

exec_dir="/net/dstore2/teraraid/dmorado/software/subTOM/bin"

fsc_exec="${exec_dir}/analysis/subtom_maskcorrected_fsc"

ref_a_fn_prefix="even/ref/ref"

ref_b_fn_prefix="odd/ref/ref"

iteration=1

fsc_mask_fn="FSC/fsc_mask.em"

filter_a_fn=""

filter_b_fn=""

output_fn_prefix="FSC/ref"

pixelsize=1

nfold=1

rand_threshold=0.8

plot_fsc=1

do_sharpen=1

b_factor=-150

box_gaussian=3

filter_mode=1

filter_threshold=0.143

plot_sharpen=1

do_reweight=0