subtom_plot_filter

Plots the filter applied to the reference from a user-specified set of band-pass settings. The filter can also be plotted in conjunction with a CTF root square function and a B-factor described exponential decay falloff curve. The plot can also be saved to disk.

This utility script uses one MATLAB compiled scripts below:

• subtom_plot_filter

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

plot_filter_exec

Plot filter executable.

File Options

output_fn_prefix

Relative path and name prefix of the output plot. If you want to skip this output file leave this set to “”.

Plot Filter Options

box_size

Size of the volume in pixels. The volume will be a cube with this side length.

pixelsize

Pixelsize of the data in Angstroms.

high_pass_fp

High pass filter cutoff (in transform units (pixels): calculate as:

high_pass_fp = (box_size * pixelsize) / (high_pass_A)

(define as integer e.g. high_pass_fp=2)

high_pass_sigma

High pass filter falloff sigma (in transform units (pixels): describes a Gaussian sigma for the falloff of the high-pass filter past the cutoff above.

low_pass_fp

Low pass filter cutoff (in transform units (pixels): calculate as:

low_pass_fp = (box_size * pixelsize) / (low_pass_A)

(define as integer e.g. low_pass_fp=48)

low_pass_sigma

Low pass filter falloff sigma (in transform units (pixels): describes a Gaussian sigma for the falloff of the low-pass filter past the cutoff above.

defocus

Defocus to plot along with band-pass filter in Angstroms with underfocus being positive. The graphic will include a line for the CTF root square and how it is attenuated by the band-pass which can be useful for understanding how amplitudes are modified by the filter. If you do not want to use this option just leave it set to “0” or “”.

voltage

Voltage in keV used for calculating the CTF. If you do not want to plot a CTF function leave this set to “” or “300”.

cs

Spherical aberration in mm used for calculating the CTF. If you do not want to plot a CTF function leave this set to “” or “0.0”.

ac

Amplitude contrast as a fraction of contrast (i.e. between 0 and 1) used for calculating the CTF. If you do not want to plot a CTF function leave this set to “” or “1”.

phase_shift

Phase shift in degrees used for calculating the CTF. If you do not want to plot a CTF function leave this set to “” or “0”.

b_factor

B-Factor describing the falloff of signal in the data by a multitude of amplitude decay factors. The graphic will include a line for the falloff and how it interacts with both the CTF if one was given and the band-pass filter. If you do not want to use this option just leave it set to “” or “0”

Example

scratch_dir="${PWD}"

mcr_cache_dir="${scratch_dir}/mcr"

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

plot_filter_exec="${exec_dir}/utils/subtom_plot_filter"

output_fn_prefix=""

box_size="192"

pixelsize="1.35"

high_pass_fp="1"

high_pass_sigma="2"

low_pass_fp="48"

low_pass_sigma="3"

defocus="15000"

voltage="300"

cs="2.7"

ac="0.07"

phase_shift="0.0"

b_factor="-130"