| -normalize | Normalize symmetrized output, use for maps close to symmetry (default not). |
| -background | Calculate new background values. |
| -project 20 | Generate projections with this angular step size (over 360 degrees). |
| -kernel 6,2 | Reciprocal space projection: kernel size and power. |
| -elliptical 37,5.5 | Elliptical distortion: major axis angle and shift (pixels). |
| -rescale -0.1,5.2 | Rescale data to average and standard deviation. |
| -helix 25.3,67.1,2 | Symmetrize: Helical rise and angle, and dyad axis indicated by 2. |
| (default 10 angstrom, 45 degrees, no dyad axis). | |
| -rule 237.5,-2,7 | Symmetrize by selection rule: Helical repeat (angstrom), turns and subunits per repeat. |
| -super 25.3,67.1,22,15.5 | Superhelix: Helical rise and angle, and offset in xy plane. |
| -seam 1.5 | Symmetrize with the given subunit shift along the seam. |
| -findrs 5,8,0.1,10,20,1 | Find helical parameters in real space: |
| rise start, end and increment, rotation angle start, end and increment. | |
| -findcc 10,22.4,1.5 | Find helical parameters by cross-correlation: |
| rotation angle start, end and increment. | |
| -segment 10,22.4,1.5,18 | Correlate helical segments: rotation angle start, |
| end, increment and segment thickness. | |
| -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). |
| -zlimits 8,47 | Range of slices along the helical axis to use (default 0,inf). |
| -radius 22 | Radial limit for symmetrization and finding parameters (default from image). |
| -resolution 15.6,200 | Resolution limits for projection and cross-correlation (default 0). |
| -bin 2 | Binning for finding parameters (default 1). |
| -Postscript file.ps | Postscript output file name. |