The CTF Graph
1. The X coordinate is normalized frequency.
1.0 equals the Nyquist frequency determined by the pixel size.
In our case the pixel
size is in nanometers, the Nyquist frequency in 1/nm would be
0.5/pixel_size.
The text field marked
with Z at the top center reports the found normalized frequency of the
first zero.
The absolute frequency of the first
zero in 1/nm is (normalized frequency)*(Nyquist frequency).
The text field marked with D at the
top center reports the found defocus in microns.
2. The red curve is the logrithm of the CTF
curve of the selected views after subtracting the noise floor.
The green curve fits the red
curve from X1_starts to X1_ends, which can be set in the fitting range
dialog.
The blue curve
fits the red curve from X2_starts to X2_ends, which can be set in the
fitting range dialog.
The intersection point of
the green curve and the blue curve is where the program finds the first
zero of the CTF.
3. To zoom in an area, hold down the
left
mouse button to
draw a rubber band around that area.
To go back to the previous
zoom
level, push the Zoom_out icon.
4.
Use arrow keys to scroll vertically and horizontally.
5. Double clicking at a point in the plot will set
the found frequency of the first zero to the frequency at point.
The found defocus field will
change accordingly. This is useful for manually locating the first zero
and finding its corresponding defocus.
Tool Button Usage
Zoom in.
Zoom out.
Bring up the fitting range
dialog.
Bring up the tilt angle
range
dialog.
Adding Non-center Strips button. If
this button is enabled, the current estimation is based only on center
strips;
push this button to add non-center strips to the current estimation.
Save
the defocus found for
the selected views in the output file. A line is added to the
output file each time this button is pressed.
Print the plotted curves.
Bring up Qt assistant to display
this page.
Fitting Range Dialog

X1 sets the fitting range for the green curve, before the first
zero. Use the radio
button to fit to a straight line or to a Gaussian.
X2 sets the fitting range for the
blue curve, after the first zero. Use the radio button to
fit to a straight line or to a Gaussian.
Push the Apply button to fit the CT curves with the current limits.
Push the Close button to close this dialog.
Tilt Angle Range Dialog

Expected defocus:
The first time this dialog is brought up, the expected defocus value
specified in the parameter file is shown.
When ctfplotter computes its first estimation, it computes the
frequency
of the first zero of the CTF curve based on this original
expected defocus. This frequency is used to set the initial values of
the X1 and X2 ranges which determine what segments of the CTF curve are
fitted.
For the subsequent estimation, ctfplotter uses a defocus to
compute shifts needed to align the CTF curves of non-center
strips with the CTF curve of center strips. With the radio button group
Which defocus to use, the user
can specify
whether to use the expected defocus shown in the Expected defocus
(um) Edit field or the defocus previously found by the
program as the defocus for computing the shifts.
Center defocus tol:
The image region with defocus difference less than this tolerance is
defined as
the center region.
Left defocus tol:
The image region to the left of the center region with defocus
difference less
than this
tolerance
will be included after the 'Adding Noncenter Strips' button is pushed,
or if the All tiles radio
button is selected.
Right
defocus tol:
The image region to the right of the center region with defocus
difference
less than this
tolerance
will be included after the 'Adding Noncenter Strips' button is pushed,
or if the All tiles radio
button is selected.
Tilt angle starts
Tilt
angle ends:
The views with tilt angle
greater than the starting angle but less than the ending angle
will be included in the estimation.
Tile size:
The tile size in pixels.
Tilt axis angle:
The amount in degrees that the tilt axis deviates from being vertical
(Y axis).
Initial tiles to include radio
button group:
Choose whether or not to include the noncenter strips in the estimation
after pushing the Apply button.
If Only central tile is
checked, after pushing the Apply
button,
only the center region defined by
Center defocus tol will be
included and the 'Adding
Non-center Strips' button will be enabled.
The user needs to push that button to add the left region defined by Left defocus tol and the right region
defined by Right defocus tol
to the estimation.
If All tiles is checked,
after pushing the Apply
button,
all regions (center, left, right) will be included in
the estimation and the 'Adding
Non-center Strips' button will be disabled.
Push the 'Store current defocus' icon to write the defocus found to the
output file.
Push the Apply button to
recompute the CTF curve with the current parameters.
Push the Close button to close
this dialog.
Refer to ctfplotter man page