| -reconstructions | Operate on reconstruction parameters rather than micrographs. |
| -list | List all micrograph and reconstruction markers. |
| -rotate 0.3,0.1,-0.5,81 | Rotate around an axis by an angle. |
| -scale 0.5,3,1 | Scale. |
| -translate 12.2,0.5,-50 | Shift after rotation and scaling. |
| -plane | Calculate a plane through the markers. |
| -fom 0.55 | Select markers with a figure-of-merit above this cutoff. |
| -verbose 7 | Verbosity of output. |
| -origin 0,22.5,30 | Set the origin for rotation. |
| -output out.star | Output micrograph parameter file. |