subtom_plot_filter

Creates a graphic of bandpass filters optionally with CTF.

subtom_plot_filter(
    'box_size', box_size (''),
    'pixelsize', pixelsize (1),
    'high_pass_fp', high_pass_fp (0),
    'high_pass_sigma', high_pass_sigma (0),
    'low_pass_fp', low_pass_fp (0),
    'low_pass_sigma', low_pass_sigma (0),
    'defocus', defocus (0),
    'voltage', voltage (300),
    'cs', cs (0),
    'ac', ac ('1.0'),
    'phase_shift', phase_shift (0.0),
    'b_factor', b_factor (0.0),
    'output_fn_prefix', output_fn_prefix (''))

Takes in the local alignment filter parameters used in subTOM, high_pass_fp, high_pass_sigma, low_pass_fp, and low_pass_sigma; then produces a figure showing the filter that will be applied to the Fourier transform of the reference during alignment. The Fourier pixel frequencies are converted into Angstroms using the given box_size and pixelsize. A single CTF can also be specified with defocus, voltage, cs, ac, phase_shift, and the root square of this curve will be plotted in addition to how the band-pass filter affects the amplitude effects of the CTF. Finally a B-factor falloff can also be specified with b_factor, and this decay curve will also be plotted and also plotted with the CTF root square, and also the CTF root square and band-pass filter all together, so a cumulative effect of a specific choice of filter parameters at a given defocus and falloff can be observed. If output_fn_prefix is not emtpy it is used to save the graphic in MATLAB figure, pdf, and png formatted files.

Example

subtom_plot_filter(...
    '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', 0, ...
    'output_fn_prefix', 'alignment_1');

See Also