ctfplotter(1) ctfplotter(1)
NAME
ctfplotter - estimate defocus values of a tilt series
SYNOPSIS
ctfplotter options
DESCRIPTION
This GUI program will plot the logarithm of the CTF curve of an input
tilt series after subtracting the noise floor. The method is based on
periodogram averaging. The user can interactively choose which projec-
tion views are included in the averaging.
The noise floor is based on actual measurements of noise in an image
taken with no specimen in the beam. Thus, in order to use this pro-
gram, you need to collect a set of such blank images, at a series of
beam intensities, and place each image in a separate file. These noise
files are specific not only to the microscope but also to the CCD cam-
era used, the operating voltage, and the binning. The mean counts in
these files should span the range of the mean counts in the data being
analyzed. The interval between intensities can be a factor of 1.5;
interpolation is used to estimate the noise for an image whose mean
counts do not match one of the noise files. For example, for a camera
that has a gain of 10 counts per electron, one might collect images at
mean counts near 100, 150, 225, etc., up to 2210. With a 1 nm pixel
size, these noise files could be used with images where the dose
recorded at the camera ranged from 0.1 to 2.2 electrons per square
Angstrom. If you need files for analyzing both unbinned and binned
data, you can take one set of unbinned noise images and then bin them
with Newstack.
If there are significant numbers of X-rays in the noise images, you
should clean them with Ccderaser, such as with:
ccderaser -find -peak 8 -diff 8 input_fle output_file
To read a general description of the plots and tool buttons, click the
handbook icon to access the HTML help page.
Found defocus values can be saved in a text file that can be used as
input to the CTF correction program ctfphaseflip.
A sample parameter file for running the program at the command line can
be found in the IMOD/com directory.
Options
Ctfplotter uses the PIP package for input (see the manual page for
pip). Options can be specified either as command line arguments
(with the -) or one per line in a command file (without the -):
-input OR -InputStack File name
Input stack whose defocus will be estimated.
-angleFn OR -AngleFile File name
File containing tilt angles for the input stack. Each line of
this file is the tilt angle for a view of the input stack. The
angles are listed in order starting from view 1.
-config OR -ConfigFile File name
The configure file specifies the noise files used to estimate
the noise floor, one file per line. The files should be speci-
fied with absolute paths; the program will not work off of the
path of the configure file itself.
-defFn OR -DefocusFile File name
File to store found defocuses. Each entry in the file will con-
sist of the starting and ending view number of the range of
views being fit to (numbered from 1), the starting and ending
angle of the tilt angle range being fit to, and the defocus
value in nanometers (underfocus positive).
-aAngle OR -AxisAngle Floating point
Specifies how much the tilt axis deviates from vertical (Y
axis). This angle is in degrees. It follows the right hand
rule and counter-clockwise is positive.
-psRes OR -PSResolution Integer
The number of points over which CTF will be computed. The
Nyquist frequency is divided into equal intervals delineated by
these points.
-tileSize OR -TileSize Integer
The tile size each strip will be tessellated into. The size is
in pixels and the tiles are square. Each view is first divided
into strips that are considered to have constant defocus.
-volt OR -Voltage Integer
Microscope voltage in kV.
-cache OR -MaxCacheSize Integer
To speed up computation, ctfplotter uses a cache to hold slices
it recently accessed. This option controls the cache size. If
the user does not specify the option, it is defaulted to
1000Megs.
-debug OR -DebugLevel Integer
Debug level, 0-3. 0: quiet. 1: user messages. 2: cache, tile
iteration messages. 3: additional fitting messages. the default
is 1.
-cs OR -SphericalAberration Floating point
Microscope spherical aberration in millimeters
-defTol OR -DefocusTol Integer
Defocus tolerance in nanometers defining the center strips. The
center strips are taken from the central region of a view that
has defocus difference less than this tolerance. These kind of
center strips from all views within AngleRange are considered to
have a constant defocus and are used to compute the initial CTF
after being further tessellated into tiles.
-pixelSize OR -PixelSize Floating point
Image pixel size in nanometers.
-ampContrast OR -AmplitudeContrast Floating point
The fraction of amplitude contrast. For Cryo-EM, it should be
between 0.07 and 0.14.
-expDef OR -ExpectedDefocus Floating point
Expected defocus at the tilt axis in nanometers, with a positive
valie for underfocus. The frequency of the first zero of the
CTF curve is first computed based on this expected defocus. The
segments of the CTF curve of the input stack around that fre-
quency are selected to be fitted.
-leftTol OR -LeftDefTol Floating point
Defocus tolerance in nanometers for strips to the left of the
center strip. When non-center strips are included in the aver-
age, strips to the left of center are included if their defocus
difference is less than the given value.
-rightTol OR -RightDefTol Floating point
Defocus tolerance in nanometers for strips to the right of the
center strip. When non-center strips are included in the aver-
age, strips to the right of center are included if their defocus
difference is less than the given value.
-range OR -AngleRange Two floats
Starting and ending tilt angles for initial analysis. Views
with a tilt angle within this range are used to compute the CTF
curve.
-param OR -Parameter Parameter file
Read parameter entries from this file.
-StandardInput
Read parameter entries from standard input
AUTHOR
Quanren Xiong
SEE ALSO
ctfphaseflip
BUGS
Email bug reports to xiongq at colorado dot edu.
BL3DEMC 3.13.2 ctfplotter(1)