| -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). |
| -resolution 900,300 | High and low resolution limits for cross-correlation (default 0.1,1000 angstrom). |
| -origin 110,50,44 | Origin for tilt axis (default 0,0,0). |
| -edge 23,12 | Smooth the edge to a given width, with gaussian decay of a given width. |
| -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). |
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