| -Rotate 0.5,15,123 | Psi, theta, and phi angles (default 0,0,0). |
| -verbose 7 | Verbosity of output. |
| -sampling 1.5,1.5,1.5 | Sampling (angstrom/pixel, a single value sets all three). |
| -resolution 15 | Resolution limit for output (angstrom). |
| -cutoff 0.5,45,1,0.5 | Resolution cutoffs for FSC, DPR, SSNR and RAB. |
| -ratio 2.5 | Radial sampling to Cartesian sampling ratio (default 1). |
| -map file.map | 3D reference file name. |
| -Mask mask.tif | Reciprocal space mask (same size as reference). |
| -output file.star | Output STAR format file. |
| -Postscript file.ps | Postscript output filename. |
| -projections proj.img | Output projection file name. |