| -com | Generate a new model from the centers-of-mass of molecules. |
| -all | Reset selection to all components before other selections. |
| -select #232@14 | Select models and components. |
| -first 22 | Select the first number of components. |
| -views local | Calculate views for components. Modes: origin: current origin, |
| com: center-of-mass origin, map: map origin, local: neigbor plane. | |
| -associate TRS,trs.pdb | Associate a component type with a file name. |
| -untangle 3.5,0.2 | Eliminate overlaps by moving molecules apart (sampling and damping factor). |
| -verbose 7 | Verbose output. |
| -separate | Each model is defined as a separate molecule group. |
| -componentradius 8.4 | Set display radius for all components. |
| -linkradius 5.1 | Set display radius for all links. |
| -reset | Reset selection to all components before other selections. |
| -parameters param.star | Input parameter file. |
| -output file.star | Output model parameter file. |
| -coordinates all.pdb | Output coordinate files. |