| -create mod1 | New model with the given ID. |
| -symmetry O-3 | New model type based on symmetry (T, O and I). |
| -shell 134.2 | Generate a spherical shell with the given radius. |
| -fibonacci 244,50 | Generate a fibonacci sphere: number of components and radius. |
| -icosahedron 238.5,3,1 | Generate an icosahedral shell with the given radius and divisions, |
| and a flag 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 88.3,155 | Generate a cylinder with the given radius and length. |
| -spindle 88.3,9.5 | Generate a spindle with the radius and packing separation. |
| -randomfill 56 | Random model with a number of non-overlapping components (use with -componentradius). |
| -randomshell 87 | Random model with a number of components on a shell. |
| -gaussian 44,30.7 | Random model with a number of gaussian distributed components and standard deviation. |
| -peaks cc.map | Generate a model from peaks in a map. |
| -all | Reset selection to all models and components before other selections. |
| -replace | Replace existing components with newly created ones (default add). |
| -reduce submod.star | Replace each set of linked components with one new component and write sub-model file. |
| -id model1 | Set model identifier. |
| -settype VER | Set all component types. |
| -changetype VER,KRN | Change component type name. |
| -add -56,3.45,-123 | Add a component (define model with -id and type with -settype). |
| -associate TRS,trs.pdb | Associate a component type with a file name. |
| -linklength 56.3 | Generate links with this maximum length. |
| -rdf 1.2 | Calculate the radial distribution function with the given sampling (angstrom). |
| -consolidate 85.4 | Consolidate models: components are considered the same if within the given distance. |
| -verbose 7 | Verbosity of output. |
| -distance 54.7 | Component distance from origin (default 100 angstrom). |
| -helix 31.6,43.2,35 | Helix with given rise, rotation angle and number of components. |
| -direction 0.2,-0.5,0.3 | Direction vector (for -cylinder and -spindle). |
| -componentradius 0.5 | Component display radius (angstrom). |
| -linkradius 0.5 | Link display radius (angstrom). |
| -color 0.1,0.5,0.2,1 | Color new models. |
| -points 152 | Number of points. |
| -separation 2.5 | Separation distance between points. |
| -parameters param.star | Input parameter file. |
| -map file.map | Input map file to associate with shell model. |
| -output newmod.star | New model file. |
| -catenate catmap.pif | New file name for catenated model maps. |