| -mode 1 | Symmetry mode: 0=during reconstruction (default), 1=after reconstruction, |
| 2=pick a random symmetry view for each particle. | |
| -TwoD | Generate a 2D reconstruction (default 3D). |
| -CTF flip | Apply CTF correction to images before reconstruction (default not). |
| -rescale -0.1,5.2 | Rescale reconstruction to an average and standard deviation. |
| -bootstrap | Use particle selection numbers to weigh their contributions. |
| -filaments | Generate one map per filament. |
| -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 100,120,90 | Size of reconstruction (default from images). |
| -sampling 1.5 | Reconstruction sampling (A/pixel; default from first particle image). |
| -scale 1.2 | Scale or magnification of reconstruction compared to original images (default 1). |
| -resolution 20 | Resolution limit (angstrom, default Nyquist). |
| -interpolation weighted | Interpolation type: nearest (default), weighted, trilinear. |
| -pad 3 | Image padding factor (default 2). |
| -symmetry D6 | Symmetry: Point group identifier |
| -wiener 0.15 | Wiener factor for CTF correction (default 0.2). |
| -reconstruction file.ext | Reconstruction file name. |
| -fom file.ext | Figure-of-merit file name. |
| -output file.star | Output parameter file name. |
| -Postscript file.ps | Postscript output filename. |