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:
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"