| -center | Center before all other operations. |
| -minimize 150 | Number of iterations for minimizing a model. |
| -dynamics 500 | Number of iterations for running dynamics on a model. |
| -all | Reset selection to all components before other selections. |
| -select #Mod1@14 | Select models and components. |
| -verbose 7 | Verbosity of output. |
| -componentradius 0.5 | Component display radius. |
| -linkradius 0.5 | Link display radius. |
| -shift 6.8 | Maximum shift per iteration (angstrom, default infinite). |
| -timestep 0.01 | Integration time step (default 0.001). |
| -velocitylimit 0.01 | Limit on the velocity (default 0.1 per time step). |
| -friction 0.2 | Friction constant (default 1 = no friction). |
| -neighbors 7,45 | Neighbor designation: number and neighborhood scale (default 8,50). |
| -Kdistance 0.1 | Distance force constant (default 0). |
| -Klink 0.01 | Link force constant (default 0). |
| -Kangle 0.1 | Angle force constant (default 0). |
| -Kpolyangle 0.1 | Polygon angle force constant (default 0). |
| -Kpolygon 0.001 | Polygon regularity force constant (default 0). |
| -Kpolyplane 0.1 | Polygon planarity force constant (default 0). |
| -Kpoint 0.1,0.02 | Point force constant and decay (default 0,0.01). |
| -Kradial 0.1 | Radial force constant (default 0). |
| -radius 212 | Reference radial distance (default 0). |
| -Kplane 0.2 | Neighbor plane force constant (default 0). |
| -Kguide 0.5 | Polyhedron guide force constant (default 0). |
| -Kmap 0.5 | Map force constant (default 0). |
| -sigma 17 | Sigma determining kernel size for fitting a map (default map pixel size). |
| -parameters parm.star | Model parameter file (default atom_prop.star). |
| -guide file.star | Polyhedron guide model file. |
| -output file.star | Output model file. |
| -writeparam dm.star | Write model parameter file. |