| -all | Reset selection to all components before other selections. |
| -select A | Select a component type. |
| -first 22 | Select the first number of components. |
| -id model1 | Select a model by its identifier. |
| -com | Generate a new model from the centers-of-mass of molecules. |
| -views | Calculate views for components. |
| -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. |
| -parameters param.star | Input parameter file. |
| -output file.star | Output model parameter file. |
| -coordinates all.pdb | Output coordinate files. |