| -merge | Merge models in different files rather than concatenate. |
| -all | Reset selection to all models and components before other selections. |
| -select #232@14 | Select models and components. |
| -center | Center before all other operations. |
| -map image.pif,2 | Map and image number associated with model. |
| -setasu D8 | Set components to within an asymmetric unit. |
| -apply T | Apply point group symmetry. |
| -symmetrize C5 | Symmetrize for a point group symmetry. |
| -separate D7 | Generate separate symmetry-related models. |
| -find 3,12 | Find component cyclic symmetry in the given order range. |
| -reset | Reset selection to all components before other selections. |
| -verbose 7 | Verbose output. |
| -componentradius 8.4 | Set display radius for all components. |
| -linkradius 5.1 | Set display radius for all links. |
| -origin 0,22.5,30 | Set the symmetry origin. |
| -annuli 3,12 | Annular range to find cyclic symmetry (pixels). |
| If not specified, taken from component radius. | |
| -width 10 | Annular width to find cyclic symmetry (pixels). |
| -parameters param.star | Input parameter file. |
| -output file.star | Output model parameter file. |
| -split 3 | Split models into individual files: |
| Argument: 1-6: number of digits inserted before extension | |
| Argument: "id": model ID's are used as file names. | |