usage: prog [options] <input stack/image> ...
Various CTF-related operations on images, including automatic fitting.Input particles should be unmasked and unfiltered. A
minimum of ~20 percent padding around the particles is required for background extraction, even if this brings the edge
of another particle into the box in some cases. Particles should be reasonably well centered. Can also optionally phase
flip and Wiener filter particles. Wiener filtration comes after phase-flipping, so if phase flipping is performed Wiener
filtered particles will also be phase-flipped. Note that both operations are performed on oversampled images if specified,
but this will produce phase-flipped images which are irreversible, so, while oversampling can be useful for fitting, it
is not recommended for phase-flipping.

Increasing padding during the particle picking process will improve the accuracy of phase-flipping, particularly for
images far from focus.

NOTE: This program should be run from the project directory, not from within the particles directory

Option Type Description
--version None show program's version number and exit
--allparticles None Will process all particle stacks stored in the particles subdirectory (no list of files required)
--onlynew None Will skip any files for which __ctf_flip files already exist.
--onlynoinvar None Will skip any files for which __ctf_flip_invar files already exist.
--sortdefocus None Sorts the micrographs in order by defocus
--minptcl int Files with fewer than the specified number of particles will be skipped
--minqual int Files with a quality value lower than specified will be skipped
--chunk str <chunksize>,<nchunk>. Will process files in groups of chunksize, and process the <nchunk>th group. eg - 100,3 will read files 300-399
--gui None Start the GUI for interactive fitting
--autofit None Runs automated CTF fitting on the input images
--wholeimage None Display an additional curve using the whole micrograph, not just particles.
--highdensity None If particles are very close together, this will interfere with SSNR estimation. If set uses an alternative strategy, but may over-estimate SSNR.
--zerook None Normally particles with zero value on the edge are considered to be bad. This overrides that behavior, primarily for simulated data.
--astigmatism None Includes astigmatism in automatic fitting
--phaseplate None Include phase/amplitude contrast in CTF estimation. For use with hole-less phase plates.
--curdefocushint None Rather than doing the defocus from scratch, use existing values in the project as a starting point
--curdefocusfix None Fixes the defocus at the current determined value (if any) (+-.001 um), but recomputes SSNR, etc.
--useframedf None Use defocus/astig from whole frame even if particle-based value is present
--bgmask int Background is computed using a soft mask of the center/edge of each particle with the specified radius. Default radius is boxsize/2.6.
--fixnegbg None Will perform a final background correction to avoid slight negative values near zeroes
--computesf None Will determine the structure factor*envelope for the aggregate set of images
--apix float Angstroms per pixel for all images
--voltage float Microscope voltage in KV
--cs float Microscope Cs (spherical aberation)
--ac float Amplitude contrast (percentage, default=10)
--defocusmin float Minimum autofit defocus
--defocusmax float Maximum autofit defocus
--constbfactor float Set B-factor to fixed specified value, negative value autofits
--autohp None Automatic high pass filter of the SNR only to remove initial sharp peak, phase-flipped data is not directly affected (default false)
--invert None Invert the contrast of the particles in output files (default false)
--nonorm None Suppress per image real-space normalization
--nosmooth None Disable smoothing of the background (running-average of the log with adjustment at the zeroes of the CTF)
--refinebysnr None Refines the defocus value by looking at the high resolution smoothed SNR. Requires good starting defocus. Important: also replaces the SNR with a smoothed version.
--phaseflip None Perform phase flipping after CTF determination and writes to specified file.
--phasefliphp None Perform phase flipping with auto-high pass filter (deprecated)
--extrapad None If particles were boxed more tightly than EMAN requires, this will add some extra padding, but only to processed output particles
--phaseflipsmall None Produce an output set with 1/2 size particles for faster initial model work (deprecated)
--wiener None Wiener filter (optionally phaseflipped) particles.
--snrfilt None Apply SNR filter as part of phase flipping.
--proctag None Tag added to the name of each particle when using the phaseflipproc options
--phaseflipproc None If specified _proc particles will be generated. Typical = filter.lowpass.gauss:cutoff_freq=.07
--phaseflipproc2 None If specified _proc particles will be generated. Typical = filter.highpass.gauss:cutoff_freq=.005
--phaseflipproc3 None If specified _proc particles will be generated. Typical = math.meanshrink:n=2
--phaseflipproc4 None If specified _proc particles will be generated.
--phaseflipproc5 None If specified _proc particles will be generated.
--compressbits int Bits to keep when writing images with compression. 0->lossless floating point. Default 6
--storeparm None Output files will include CTF info. CTF parameters are used from the database, rather than values that may be present in the input image header. Critical to use this when generating output !
--oversamp int Oversampling factor
--classify int Highly experimental ! Subclassify particles (hopefully by defocus) into n groups.
--sf str The name of a file containing a structure factor curve. Specify 'none' to use the built in generic structure factor. Default=auto
--parallel None parallelism argument. This program supports only thread:<n>
--threads int Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful
--debug None None
--dbds str Obsolete option for old e2workflow. Present only to provide warning messages.
--source_image str Filters particles only with matching ptcl_source_image parameters in the header
--ppid int Set the PID of the parent process, used for cross platform PPID
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness

For more information go to emanwiki/EMAN2/Programs/e2ctf.