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

zoominButton         Zoom in.
zoomoutButton       Zoom out.
rangButton  Bring up the fitting range dialog.
angleButton  Bring up the tilt angle range dialog.
  moretileButton    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.
saveButton     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.
printerButton  Print the plotted curves.
helpButton       Bring up Qt assistant to display this page.


Fitting Range Dialog

rangeDialog

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

angleDialog
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