| -fom 0,1.0,0.0 | Rescale FOM to min and max and apply cutoff. |
| -weigh | Weigh the amplitudes with the FOM. |
| -translate 0.0,0.0,0.0 | Translation in fractional coordinates. |
| -analyze | Analyze structure factors. |
| -mirror | Mirror = invert Friedel symmetry. |
| -normalize | Normalize to average amplitude. |
| -scale file.hkl | Scale SF with profile from input SF. |
| -combine file.hkl | Combine SF with profile scaling with input SF. |
| -symmetry 1 | Check symmetry for this space group. |
| -Symmetry 1 | Apply symmetry for this space group. |
| -verbose 7 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -sampling 2,3.5,1 | Sampling (angstrom/voxel, a single value sets all three). |
| -resolution 6.5 | Resolution in A (default maximum in data). |
| -unitcell | 96,96,100,90,90,90 Unit cell parameters. |
| -free 15 | % flagged for R-free calculations (default 10%). |