| -mode | refine Search, Refine or Extract. |
| Search: Searches the particles in the input.image. | |
| Refine: Refines the orientations of the particles in the input.star. | |
| Extract: Writes selected particles to image files. | |
| -transform | Transform the particle before extraction (use only in Extract mode). |
| -inverse | Transform the template instead of the particle (use only in Extract mode). |
| -star | Output a star file for each extracted particle (use only in Extract mode). |
| -wedges | Output rotated missing wedge masks for each particle (use only in Extract mode). |
| -iterate | 2 Iterate angular refinement (default 1 iteration). |
| The original step sizes and limits are halved after every iteration (use only in Refine mode with angle limits). | |
| -verbose | 7 Verbosity of output. |
| -datatype | u Force writing of a new data type (default is float). |
| -sampling | 1.5,1.5,1.5 Sampling (A/pixel; default from input file; a single value can be given). |
| -origin | 110,50,44 Origin for rotations of the template (default taken from template image). |
| -convert | Convert the first particle in the star-file into a reconstruction. |
| -angles | 8.8,2.5,5.2 Step size for alpha, theta and phi, one value sets all (default 45 degrees). |
| -alphalimit | 30 Angular limit for alpha (default: 180 degrees). |
| -thetaphilimit | 5 Angular limit for theta & phi (default: 180 degrees, cannot be used with option symmetry). |
| -shiftlimit | 5 Radial limit to search for shift in cross-correlation map, around the location given in input.star. |
| (pixels; default: whole map in Search mode, 1/2 template in Refine mode). | |
| -resolution | 15.6,200 Resolution limits for cross-correlation (default 0). |
| -symmetry | I Symmetry of the template (default: no symmetry, thetaphilimit used instead). |
| -bin | 3 Binning of input, template and mask by given kernel size, |
| output image remains same size as input. | |
| -refinepeaks | Refine peaks from cc search to subpixel accuracy. |
| -threshold | 0.5 Report only particles above the ccc threshold. |
| -maxhits | 10 Maximum number of particles to report for each orientation (default: all). |
| -zshiftlimit | 10 Shift allowed in addition to 'shiftlimit' in the direction of the view vector (Use only in Refine mode, no xyshiftlimit). |
| -xyshiftlimit | 10 Shift allowed in addition to 'shiftlimit' in the orthogonal to the view vector (Use only in Refine mode, no zshiftlimit). |
| -all | Reset selection to all particles before other selections. |
| -mindist | 64 Discard overlapping particles (default: size of the template in Search, selection number set to zero). |
| -minangledif | 50 Discard particles with too similar orientations (selection number set to zero). |
| -fom | 0.3 Discard particles below the threshold (selection number set to zero). |
| -spheremindist | 5 Discard particles too far from a sphere that best fits all the particles (selection number set to zero). |
| -topp | 75.0 Select only the best percentage of particles (default 100%). |
| -topn | 100 Select only a number of best particles from each reconstruction (default all). |
| -withindist | 100,100,100,45 Select only particles within a set distance from a point. |
| -remove | Remove all particles with selection number 0 after other selections. |
| -renumber | Renumber particles. |
| -select | 1 Extract particles with this selection number (default: all > 0). |
| -size | 50,50,50 New size for transformed particles (use only in Extract mode. one value sets all). |
| -partpath | dir/subdir Set the particle file paths (use only in Extract mode). |
| -partextension | pif Set the particle image file format (dafault: map. use only in Extract mode). |
| -Template | image.map Template to search for or to refine. |
| -mask | mask_1.map Mask in real space to apply on template. Use a soft edged mask. |
| -Mask | mask_2.map Mask in reciprocal space to apply during cross-correlation and for CCC normalization. |
| -output | file.star Output parameter file with orientations. |
| -ccmax | ccmax.img Output image with maximum cross-correlation coefficient value for each position (use only in Search mode). |