| -rescale -0.1,5.2 | Rescale data to average and standard deviation. |
| -edge | Smooth map with an oval edge. |
| -classes 1,3-5 | Class selection: can be all, selected, or any combination of numbers (default selected). |
| -fullmap | Output one full map per class (default if -halfmaps not used). |
| -halfmaps | Output 2 maps from half sets. |
| -threads 2 | Threads per class (default 1, must be even for -halfmaps). |
| -verbose 7 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -size 120,120,80 | Output 3D volume size (default from input file). |
| -sampling 2,3.5,1 | Sampling (angstrom/voxel, a single value sets all three). |
| -scale 1.2 | Scale or magnification of reconstruction compared to original images (default 1). |
| -resolution 3.4 | Resolution (angstrom). |
| -symmetry D6 | Symmetry: Point group identifier. |
| -reconstruction file.map | Output 3D reconstruction. |
| -output file.star | Output parameter file name. |