| -find opp | Type of correlation: worst, opposite, c5. |
| -analyze 0.1 | Calculate statistics for vertices. |
| -verbose 7 | Verbosity of output. |
| -resolution 15.6,200 | Resolution limits for cross-correlation (default 0,inf). |
| -maxresolution 9.5 | Maximum reconstruction resolution limit (default Nyquist). |
| -reference image.map | Reference for cross-correlation. |
| -mask image.map | Real space mask. |
| -Mask fsmask.mrc | Frequency space mask (missing data). |
| -special vert.star | Parameter file with special vertex orientations. |
| -output file.star | Output parameter file. |
| -reconstruction file.ext | Reconstruction file name. |