| -shell 134.2 | Generate a shell with the given radius. |
| -dodecahedron 215,3,0.3 | Generate an dodecahedral shell with the given radius and divisions, |
| and a fraction to make it spherical. | |
| -icosahedron 238.5,3,0.5 | Generate an icosahedral shell with the given radius and divisions, |
| and a fraction to make it spherical. | |
| -circle 527,243 | Generate a circle with the given radius and z offset. |
| -ellipse 620.5,314.9,5.2 | Generate an ellipse with the given x and y semi-axes lengths and z offset. |
| -ellipsoid 24.3,51.2,68 | Generate an ellipsoid with the given x,y,z semi-axes. |
| -cylinder 0,1,0,88.3,155 | Generate a cylinder with the given direction, radius and length. |
| -add -14.7 | Add a shell offset by a radial distance from selected components. |
| -fromcomponents 18.6,1 | Generate shells from components with given radius and flag for 2D. |
| -merge | Merge models into one after all other operations. |
| -guide poly.star | Input guide polyhedron to adjust the shell model. |
| -linklength 56.3 | Generate links with this maximum length for the sphere model. |
| -views local | Calculate views for components. Modes: origin: current origin, |
| com: center-of-mass origin, map: map origin, local: neigbor plane. | |
| -rdf 1.2 | Calculate the radial distribution function with the given sampling (angstrom). |
| -fit 15.6,200,1 | Fits a shell model to a map using the given resolution limits, |
| and a flag to indicate negative contrast. | |
| -radial | Calculate a radial profile based on a shell model. |
| -powerspectrum out.map | Calculate 2D power spectra around components in the shell. |
| -all | Reset selection to all models and components before other selections. |
| -select #Mod1@14 | Select models and components. |
| -verbose 7 | Verbose output. |
| -id model1 | Set model identifier. |
| -newtype MEM | Type for all new components. |
| -componentradius 0.5 | Component display radius. |
| -linkradius 0.5 | Link display radius. |
| -points 152 | Number of points. |
| -separation 2.5 | Separation distance between points. |
| -fraction 0.6 | Fraction of adjustment to a guide model (default 1). |
| -curved | Flag to indicate curved hull or shell surface (default not). |
| -size 45,40,20 | Size of densities to extract (default 20,20,20 voxels). |
| -origin 0.8,-10,15.7 | Set the origin for extracted densities. |
| -fftsize 256 | Size of power spectrum (default from images). |
| -resolution 20,360 | High and low resolution limits for cross-correlation (angstrom). |
| -annuli 2,95 | Real space annular limits (default 0,inf pixels). |
| -parameters param.star | Input parameter file. |
| -map file.map | Input map file to associate with shell model. |
| -output file.star | Output model parameter file. |