| -pick cc | Picking type: cc, var, ring, background (default none). |
| -orient ref.pif | Orient using a reference map. |
| High resolution and symmetry determine number of projections. | |
| -center | Center each particle image (specify resolution limits). |
| -axis 5,13.6 | Pick on a symmetry axis and distance along the axis (voxels, specify -symmetry). |
| -extract 0.5 | Extract particles into new images at the given scale. |
| -split | Split particles into individual files on extraction. |
| -reconstructions | Operate on reconstruction parameters rather than micrographs. |
| -project | Project 3D particles to 2D and assign to zero-tilt micrograph. |
| -add | Adjust micrograph coordinates to particle origins. |
| -filterextremes | Filter extremes before picking or centering. |
| -background | Correct background of extracted particles. |
| -normalize | Normalize extracted particles. |
| -delete | Delete all non-selected particles. |
| -verbose 7 | Verbosity of output. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; a single value can be given). |
| -origin 0.8,-10,15.7 | Set the origin (default from input image). |
| -box 123,145,130 | Particle box size (voxels, one sets all). |
| -resolution 23.5,200 | Resolution limits for picking and centering (default 0 - 1e6 angstrom). |
| -fill 127 | Fill value for particles extending beyond image (default background). |
| -mgpath dir/subdir | Set the micrograph file paths. |
| -pspath dir/subdir | Set the power spectrum file paths. |
| -partpath dir/subdir | Set the particle file paths. |
| -base subvol | Set the particle base file name (no extension). |
| -extension pif | Set the particle image file format. |
| -average 11 | Averaging/smoothing kernel size. |
| -exclusion 210 | Minimum distance between particles (default 0.8*x-size). |
| -bin 2 | Binning to apply (default 1). |
| -fom 0.1,0.8 | Selecting picked particles based on an FOM range (default 0,1e30). |
| -variance 51 | Calculate a local variance image using the given size kernel. |
| -sigma 2.5 | Sigma units above average to select particles (default 5). |
| -maximum 241 | Maximum number of background areas to pick (default 1000000). |
| -diameters 115,130 | Particle and background ring diameters. |
| -contrast black | Foreground (particles) are white or black (default). |
| -angle 2.5 | Angular increment (default 1 degree). |
| -symmetry C5 | Point group symmetry (used with -orient and -axis). |
| -Template file.map | Input template file for picking by cross-correlation. |
| -Mask file.map | Input frequency space mask file. |
| -compare file.star | Input parameter file for comparison. |
| -output file.star | Output parameter file. |