| -rescale -0.1,5.2 | Rescale data to average and standard deviation. |
| -variancemask 45 | Mask from local variance of reference with given kernel size. |
| -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). |
| -aligned 25 | Resolution limit for alignment (angstrom). |
| -fsccut 0.8,0.5,0.143 | Resolution cutoffs for FSC. |
| -dprcut 45,70 | Resolution cutoffs for DPR. |
| -ratio 2.5 | Radial sampling to Cartesian sampling ratio (default 1). |
| -map file.map | 3D reference file name. |
| -mask mask.tif | Real space mask (same size as reference). |
| -output file.star | Output STAR format file. |
| -Postscript file.ps | Postscript output filename. |
| -XML file.xml | XML output filename. |
| -tsv file.tsv | Tab-separated values output filename. |