| -crosssection | Calculate a cross section based on helical parameters. |
| -extrude 254 | Extrude the cross section to the indicated length. |
| -symmetry C5 | Apply point group symmetry. |
| -rescale -0.1,5.2 | Rescale data to average and standard deviation. |
| -verbose 1 | 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 helix (default 0,0,0 or from image). |
| -helix 25.3,67 | Helical rise and angle (default 10 angstrom, 45 degrees). |
| -resolution 15.6 | High resolution limit for reconstruction (default 0). |
| -scale 1.5 | Reconstruction scale (default 1). |
| -snradius 36 | Radius to distinguish signal from noise (alternative to -kernel). |
| -kernel 9 | Local variance kernel size for generating a foreground mask (default 11). |
| -alignresolution 20,360 | High and low resolution limits (angstrom). |
| -annuli 12,60 | Real space annular limits (default 0,inf pixels). |
| -shiftlimit 3.5 | Limit on origin shift relative to nominal center (default 10% of box edge size). |
| -fill 1.77 | Fill value for background: average (default), background, or value. |
| -reference file.map | 2D reference image file name. |