| -bin 3,2,1 | Binning by the given kernel size - one value = isotropic binning. |
| (i.e., 2 = binning with a 2x2 kernel, changes the units). | |
| -align 56 | Align to this reference image (image numbers start at 0). |
| -filament 5.3,50 | Box particles along filaments with this interval and mask width (voxels). |
| -extract 150,111,120 | Extract particles with this size (voxels, one sets all). |
| -verbose 7 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; a single value can be given). |
| -origin 110,50,44 | Origin for tilt axis (default 0,0,0). |
| -frames | Flag to align micrograph frames. |
| -dose 2.5 | Weigh the amplitudes by accumulated dose using the given dose/frame (e/Å2). |
| -exposure 8.5 | Exposure time to calculate drift rate from alignment (seconds) |
| -rate 4.5 | Frame rate (frames/second) |
| -counts | Flag to rescale images based on their counts histogram. |
| -resolution 900,300 | High and low resolution limits for cross-correlation (default 0.1,1000 angstrom). |
| -shiftlimit 3.5 | Limit on origin shift relative to nominal center (default 10% of box edge size). |
| -edge 23,12 | Smooth the edge to a given width, with gaussian decay of a given width. |
| -subset 2-8,12 | Subset of micrographs to align and average. |
| -fill 127 | Fill value for particles extending beyond image (default background). |
| -partbase subvol | Set the particle base file name (no extension). |
| -partpath dir/subdir | Set the particle file paths. |
| -partextension pif | Set the particle image file format extension. |
| -helix 16.2,39.5 | Helical parameters for filament boxing: helical rise |
| and angle per asymmetric unit (angstroms and degrees). | |
| -background | Correct background of extracted particles. |
| -normalize | Normalize extracted particles. |
| -Gainreference gr.tif | Gain reference to correct the input micrographs. |
| -Mask mask.tif | Mask file to use for cross-correlation. |
| -output file.star | Output parameter file, if -average, also output average parameter file. |
| -write sum | Output either aligned frames, sum or avg. |
| -image file.pif | Output multi-image file with aligned images. |
| -average file.pif | Output average of aligned images. |