| -reconstructions | Operate on reconstruction parameters rather than micrographs. |
| -center 85 | Center filament nodes with the given window width. |
| -density 25 | Estimate filament density per length with the given filament width. |
| -extract 150,y | Extract filaments with this width (voxels) along an axis (optional). |
| -split | Split filaments into individual files. |
| -box 125,125,1 | Box particles along filaments with this size (voxels, one sets all). |
| -interval 25.5 | Interval of boxes (default: box radius). |
| -maskwidth 50 | Width to mask boxed images (voxels). |
| -background | Correct background of extracted particles. |
| -normalize | Normalize extracted particles. |
| -rotate y | Rotate particles from filaments to align with an axis. |
| -powerspectrum 200 | Calculates average power spectra from extracted particles with optional padding. |
| -verbose 7 | Verbosity of output. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; a single value can be given). |
| -base fil_001 | Set the filament/particle base file name (no extension). |
| -path dir/subdir | Set the filament/particle file paths. |
| -extension pif | Set the filament/particle image file format. |
| -helix 16.2,39.5 | Helical parameters for filament boxing: helical rise |
| and angle per asymmetric unit (angstroms and degrees). | |
| -fill 127 | Fill value for particles extending beyond image (default background). |
| -output file.star | Output parameter file. |
| -Densities img.mrc | One dimensional image with filament densities. |
| -Postscript plot.ps | Histogram of filament densities. |