| -consolidate mod.star | Consolidate project and model parameters. |
| -images | Convert particle images (use with -outmodel). |
| -submodels | Generate particle models (use with -outmodel). |
| -verbose 7 | Verbosity of output. |
| -sampling 1.5,1.5,1.5 | Sampling of images (A/pixel; a single value can be given). |
| -template model.star | Template to associate with each particle. |
| -output newmg.star | New micrograph parameter file. |
| -outmodel partmod.star | New model file from particles. |
| -outmark markmod.star | New model file from markers. |