| -reconstructions | Operate on reconstruction parameters rather than micrographs. |
| -renumber | Renumber particles starting from 1 for each micrograph or reconstruction. |
| -all | Reset selection to all particles before other selections. |
| -consolidate | Consolidate selection under one selection number. |
| -setnumber 3 | Select given selection number and set others to zero. |
| -setfom 0.3 | Set the FOM (must be in the range 0-1). |
| -group 3022 | Select particles belonging to this group. |
| -sets 20,1 | Generate sets of this size of selected particles, |
| with a flag not to select across micrograph or reconstruction boundaries. |
| -series 25,1 | Select: Particles that are all selected in a series and generating sets. |
| with a flag not to select across micrograph or reconstruction boundaries. |
| -alternate 3 | Select: Assign successive particles to different numbers. |
| -reselect psi,0.1,0.9 | Reselect based on a range of values associated with this tag. |
| -View 0.2,-0.5,0.3,15 | Select: Within an angular distance from a view: x,y,z,angle. |
| -sideview 17.8 | Select: Side views within an angular distance from the equator. |
| -Euler 2,50,-30,2,0,40 | Select: Euler angle ranges: psi, theta, phi. |
| -rank 4,1 | Select a number of groups from FOM ranking and flag to adjust for defocus. |
| -fom 0.25,1 | Select: FOM cutoff and flag to adjust for defocus. |
| -cv 0.55,1 | Select: Cross validation cutoff and flag to adjust for defocus. |
| -top 12.0,1 | Select: percentage of particles (default 100%), ranked by FOM[index] (default index = 0). |
| -deviation -2.0,1 | Select: FOM >= average + factor*standard_deviation, using FOM[index] (default index = 0). |
| -angle 2.4 | Select: difference angle between view vectors in focal or tilt series. |
| -closesttofocus | Select: Particles from micrographs closest to focus. |
| -furthestfromfocus | Select: Particles from micrographs furthest from focus. |
| -random 23.6 | Select: random selection to get the given fraction or percentage. |
| -bootstrap 527 | Select: random selection with replacement up to the given number. |
| -Fomfirst | Set orientations to first FOM in field-of-view series. |
| -Fombest | Set orientations to best FOM in field-of-view series. |
| -filament | Check filament directions and sets consistent angles. |
| -getselection | Prints all the selection numbers. |
| -show 3 | Show particle parameters indicated by the selection number. |
| -Fomhistogram | Show FOM histogram. |
| |