ctfphaseflip General Commands Manual ctfphaseflip
NAME
testctffind - find CTF parameters with Ctffind library
SYNOPSIS
testctffind options inputFile
DESCRIPTION
This program is a relatively simple wrapper to do CTF fitting with the
Ctffind library in IMOD, which was derived from the Ctffind program of
Rohou and Grigorieff. The options essentially replicate the basic
entries to Ctffind, except that pixel size is determined from the image
file header instead of being entered. Also, there is an option -low-
dose that should be used for lower dose images (e.g., from tilt
series). Without it, this program closely matches the performance of
Ctffind 4.1.14; the option restores the better performance of Ctffind
4.1.8 for such images.
When the program is run with a single image, it outputs all information
with a text descriptions. When it is run with a multi-image file, it
outputs a table of the following values on each line:
Defocus 1 and 2 in Angstroms (astigmatism is 1 minus 2)
Astigmatism angle in degrees
phase shift in radians
cross-correlation score of the fit
Resolution to which Thon rings fit, in Angstroms
Resolution at which CTF aliasing is detected
OPTIONS
Testctffind 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 -), except
that the input file must be entered as a command-line (non-option)
argument. Options can be abbreviated to unique letters; the currently
valid abbreviations for short names are shown in parentheses.
-volt (-v) OR -Voltage Floating point
Microscope voltage in kilovolts (default 200)
-sph (-sp) OR -SphericalAberration Floating point
Spherical aberration in mm (default 2)
-box (-b) OR -BoxSize Integer
Size of spectrum to analyze. Images will be reduced to this
size unless the -resamp option is used. The box size should be
increased if CTF aliasing is detected at a resolution lower than
that to which the Thon rings fit. The default is 256.
-rmin (-rmi) OR -MinimumResolution Floating point
Minimum resolution in Angstroms, the low frequency limit of the
range to analyze. The default is 50 A.
-rmax (-rma) OR -MaximumResolution Floating point
Maximum resolution in Angstroms, the high frequency limit of the
range to analyze. The default is 10 A.
-dmin (-dmi) OR -MinDefocus Floating point
Minimum defocus of search range in Angstroms (default 5000)
-dmax (-dma) OR -MaxDefocus Floating point
Maximum defocus of search range in Angstroms (default 80000)
-dstep (-ds) OR -DefocusStepSize Floating point
Size of defocus search step in Angstroms (default 500)
-fast (-f) OR -FastSearch
Use faster, less accurate search method
-atol (-at) OR -AstigmatismTolerance Floating point
Astigmatism tolerance; limit on amount of astigmatism in
Angstroms
-known (-k) OR -AstigmatismIsKnown
Astigmatism is known; use this option to prevent astigmatism
search
-astig (-as) OR -KnownAstigmatism Floating point
Known astigmatism in Angstroms. The default is 0, so there is
no need to enter this option or the next one if -known is
entered just to prevent the astigmatism search
-angle (-an) OR -AstigmatismAngle Floating point
Known astigmatism angle in degrees (default 0)
-noex (-n) OR -NoExtraComputations
Skip extra computations used to assess the resolution that Thon
rings fit to or the resolution at which CTF aliasing is
detected.
-lowdose (-l) OR -LowDoseImages
Input images are relatively noisy; this option makes the program
skip a weighting of the power spectrum that attenuates lower
frequencies. The Ctffind program started showing poorer perfor-
mance for doses under ~10 electrons/pixel or ~3 electrons/square
Angstrom in version 4.1.9 because of this weighting. This
option restores the performance to what it was in 4.1.8. It
should be used for tilt series images.
-phase (-pha) OR -FindPhaseShift
Find additional phase shift
-phmin (-phmi) OR -MinimumPhaseShift Floating point
Minimum phase shift to search, in radians. A negative value
must be entered to find a negative phase shift.
-phmax (-phma) OR -MaximumPhaseShift Floating point
Maximum phase shift to search, in radians
-phstep (-phs) OR -PhaseStepSize Floating point
Phase shift search step in radians (default 0.1)
-resamp (-re) OR -ResampleSpectrum Floating point
Resample amplitude spectrum to the given resolution in
Angstroms. In practice, this means that the spectrum is com-
puted within a box that is larger than the final box size by
half of this value divided by the pixel size, and the final box
is extracted from this larger box.
-sec (-se) OR -SectionRangeToDo Two integers
Starting and ending section numbers to analyze, numbered from 0
-param (-pa) OR -ParameterFile Parameter file
Read parameter entries from this file.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input
HISTORY
The library was originally extracted from Ctffind 4.1.9 in 2018, with
improvements that were contributed to the main Ctffind source code.
AUTHOR
David Mastronarde
SEE ALSO
ctfplotter
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.2.0 ctfphaseflip