| -check | Check particle records. |
| -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. |
| -none | Unset selection to all particles before other selections. |
| -mgselect 3-5,8,12-15 | Select micrographs: |
| Argument: 4-11,34: Select by the indicated micrographs (first = 1). |
| Argument: part: Select only micrographs with selected particles. |
| -divide 3 | Divide the project into a number of subsets of fields. |
| -consolidate 5 | Consolidate selection under the given 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). |
| -setasu D3 | Set the views to the asymmetric unit. |
| -setgroups | Transfer selection numbers to groups. |
| -fixdefocus 0.15 | Reset particle defocus differing from micrograph defocus. |
| -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. |
| -frames 3,11 | Select: Particles from a series of frames of a field-of-view. |
| -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. |
| -origin 150,150,0,8 | Select: Within a distance from the nominal origin: x,y,z,distance. |
| -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. |
| -exclusion 210 | Select: Deselect overlapping particles (default 0). |
| -top 12.0,1 | Select: number or % particles and flag to adjust for defocus, ranked by FOM[index]. |
| -deviation -2.0 | Select: FOM >= average + factor*standard_deviation, using FOM[index]. |
| -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 number, |
| number in groups (g), fraction (<1) or percentage (%). |
| -bootstrap 527 | Select: random selection with replacement up to the given number. |
| -views 4.5,7.2,3 | Select: random selection within views defined on a grid with the |
| given theta and phi step sizes (degrees) and up to the given number. |
| -bestviews 4.5,7.2,3 | Select: best particles within views defined on a grid with the |
| given theta and phi step sizes (degrees), up to the given number. |
| -maxsmooth 0.7,3,5,4.4 | Select: above fraction specified by smoothed maxima surface. |
| given theta and phi step sizes and smoothing sigma (degrees). |
| -Fomfirst | Set orientations to first in field-of-view series. |
| -Fombest | Set orientations to best FOM[index] in field-of-view series. |
| -filament 60 | Selects filament particles with clear direction based on percentage. |
| -deselect 4,6,22 | Deselect particles with the listed selection numbers. |
| -getselection | Prints all the selection numbers. |
| -show particle.fom | Show particle parameters indicated by the tag or selection number. |
| -Fomhistogram 100,0.1.2 | Show FOM histogram with parameters: bins, minimum and maximum. |
| -focus | Show defocus minimum and maximum. |
| -reset defocus | Reset particle defocus to micrograph defocus. |
| -delete | Delete all non-selected particles from the parameter file. |
| -remove | Do not write non-selected micrographs into the parameter file. |
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