| -verbose 1 | Verbosity of output. |
| -select 14 | Selection number of particles to process (default all selected). |
| -symmetry C5 | Point group symmetry. |
| -angles 2.5,5.2 | Step size for theta and phi, one value sets both (default 45 degrees). |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; a single value can be given.) |
| -resolution 20,360 | High and low resolution limits (angstrom). |
| -polarresolution 23.5 | Resolution limit for in-plane angular alignment (angstrom). |
| -bands 250,-1,150,1,30,0 | Bands for analysis in reciprocal space (pairs of numbers: angstrom,flag). |
| Band with 0: Not used - end flag. |
| Band with 1: Use for orientation determination. |
| Band with -1: Use for cross-validation. |
| -annuli 2,95 | Real space annular limits (default 0,inf pixels). |
| -shiftlimit 3.5 | Limit on origin shift relative to nominal center (default 10% of box edge size). |
| -rotationlimit 16.7 | Limit on in-plane rotation change from input orientation (default not applied). |
| -edge 125 | Edge mask radius using previous particle origins (default not used). |
| -fom 0.3 | Set FOM threshold for selection (default 0). |
| -nothreads | Do not use threads (default parallel processing). |
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