| -merge | Merge models in different files rather than concatenate. |
| -views local | Calculate views for components. Modes: origin: current origin, |
| com: center-of-mass origin, map: map origin, local: neigbor plane. | |
| -invert | Invert views for selected components. |
| -setasu D6 | Set components to within an asymmetric unit. |
| -directions 10,1 | Histogram of component view directions with histogram bin width (degrees) |
| and a flag: 0=wrt z-axis, 1=wrt component locations. | |
| -setfom 0.8 | Set the FOM of selected components to a specific value. |
| -all | Reset selection to all models and components before other selections. |
| -select #232@14 | Select models and components. |
| -verbose 7 | Verbose output. |
| -componentradius 8.4 | Set display radius for all components. |
| -linkradius 5.1 | Set display radius for all links. |
| -combined | The views for all models are combined (-Postscript option). |
| -separate | Each model is defined as a separate molecule group (-coordinates option). |
| -parameters param.star | Input parameter file. |
| -output file.star | Output model parameter file. |
| -split 3 | Split models into individual files: |
| Argument: 1-6: number of digits inserted before extension | |
| Argument: "id": model ID's are used as file names. | |
| -coordinates all.pdb | Output coordinate files. |
| -Postscript plot.ps | Output postscript file with a plot of views. |