| -all | Reset selection to all particles before other selections (default not). |
| -shift | Center the actual particle images (default not). |
| -verbose 7 | Verbosity of output. |
| -select 14 | Selection number of particles to process (default all selected). |
| -resolution 10,500 | Resolution limits for cross-correlation (angstrom, default 20,1000). |
| -output file.star | Output parameter file. |
| -reference file.pif | Composite image reference file. |