CTF_profile

CTF profile

Purpose

This utility allows you to plot a CTF profile along any direction (since the CTF may be astigmatic). The output is dumped to stdout so it may be redirected to a file. The functionality of this program has been greatly improved by CTF_view.

Usage

$ ctf_profile -i [CTF description file] ...

Parameters

• `` Input description of the CTF. This is usually the output ofAdjust_CTF
• -w_dir "[X1,Y=0]" = Direction vector of the plot. By default, the profile along the X axis
• -w_step [step0.001] = Sampling rate in the digital frequency. This frequency is normalized to 0.5

Examples and notes

Plot of a CTF along X axis

$ CTF_profile -i piece_arma_model00001.param > CTF.plot

wherepiece_arma_model00001.param is:

sampling_rate=        3.68
voltage=              200
defocusU=             -33797.8
defocusV=             -28344.8
azimuthal_angle=      210.124
spherical_aberration= 2
chromatic_aberration= 0
energy_loss=          0
lens_stability=       0
convergence_cone=     0.0944014
longitudinal_displace=0
transversal_displace= 0
Q0=                   -1.01194e-09
K=                    0.541223
gaussian_K=           8.03264e-07
sigmaU=               42536.2
sigmaV=               49993.1
cU=                   0.0306159
cV=                   0.01
gaussian_angle=       1.21502e-10
sqrt_K=               12.4559
sqU=                  13.6719
sqV=                  12.0607
base_line=            0.658807

The first column is the digital frequency normalized to 1/2, the second the continuous frequency in (1/angstrom), the third the continuous frequency in (angstrom), the fourth corresponding part to the CTF, the fifth the corresponding to the noise background, the sixth the sum of the background noise plus the square of the CTF (this is the spectral power density).

To plot this file use:

$ gnuplot
$ gnuplot> plot "CTF.plot" u 1:4 title "CTF" w l
$ gnuplot> set xrange [0.01:]
$ gnuplot> set xlabel "Frequency (1/angstrom)"
$ gnuplot> plot "CTF.plot" u 2:5 title "Noise background" w l, "CTF.plot" u 2:6 title "Spectral power density" w l 

/ctf_profile.gif

--Main.AlfredoSolano - 17 Jan 2007