| -all | Reset selection to all particles before other selections (default not). |
| -symmetry C5 | Search for the best symmetry-related orientations. |
| -magnification 0.01 | Turns on magnification refinement: Maximum adjustment (default 0). |
| -defocus 0.002 | Turns on defocus refinement: Standard deviation for Monte Carlo, |
| Step size for grid search (default 0 um). | |
| -monte 80 | Monte Carlo with a maximum number of iterations. |
| -grid 2.5,0.3 | Grid search with angular step size and accuracy (both in degrees). |
| -verbose 7 | Verbosity of output. |
| -select 14 | Selection number of particles to process (default all selected). |
| -fomtype dpr | Resolution measurement type: frc (default), dpr. |
| -resolution 20,250 | High and low resolution limits (angstrom). |
| -kernel 11,3 | Interpolation kernel width and power (default 8,2) |
| -edge 125 | Edge mask radius using previous particle origins (default not used). |
| -nothreads | Do not use threads (default parallel processing). |
| -shift 0.4 | Random origin shift standard deviation (default 0.1 pixels). |
| -view 0.02 | Random view shift standard deviation (default 0.01). |
| -angle 0.7 | Random rotation angle maximum adjustment (default 0.5 degrees). |
| -step 1.5,0.3 | Grid search shift step size and accuracy (default 0.4,0.1 pixels). |
| -reference file.ext | Input 3D reference map file. |
| -mask mask.map | Real space 2D mask to be applied to particles. |
| -FSC file.xml | FSC curve used to weigh FOM contributions. |
| -output file.star | Output parameter file. |
| -ppx | Write temporary particle parameter files to directory "ppx". |