| -add | Adjust micrograph coordinates to particle origins. |
| -zflip | Invert the particle z coordinate before transfer. |
| -transfer mg | Calculate micrograph particle coordinates from micrograph (mg) or reconstruction (rec). |
| -reconstruct | Reconstruct individual particles from micrographs. |
| -removemarkers 14 | Mask out markers with this radius (pixels) before reconstruction. |
| -nloo 34.7,0.3 | Determine particle resolution up to the given limit and with the given cutoff. |
| -verbose 7 | Verbosity of output. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; default from parameter file; a single value can be given). |
| -views | Use particle views during transfer. |
| -boxsize 55 | Set the particle box size (default from parameter file). |
| -maxresolution 20 | Reconstruction resolution limit (angstrom, default Nyquist). |
| -interpolation weighted | Interpolation type: nearest (default), weighted, trilinear. |
| -pad 3 | Image padding factor (default 2). |
| -CTF flip | Apply CTF correction to images before reconstruction (default not). |
| -wiener 0.15 | Wiener factor for CTF correction (default 0.2). |
| -symmetry C5 | Point group symmetry. |
| -base subvol | Set the particle base file name (no extension). |
| -path dir/subdir | Set the particle file paths. |
| -extension pif | Set the particle image file format. |
| -ratio 2.5 | Radial sampling to Cartesian sampling ratio (default 1). |
| -fast 10 | Fast mode, only use micrographs within the given angle from the selected one (default all). |
| -output file.star | Output parameter file. |
| -Postscript file.ps | Output plot file. |