| -listmodels | List model information in table form. |
| -listcomponents | List component counts in table form. |
| -showmass | Show model masses. |
| -axes | Calculate principal axes. |
| -delete B | Delete a component type. |
| -setfom 0.8 | Set the FOM of selected components to a specific value. |
| -center | Center before all other operations. |
| -average 4 | Average sequential components and delete all but one in each set. |
| -histogram 0.2 | FOM histogram with the given step size. |
| -id model1 | Set model identifier. |
| -map image.pif,2 | Map and image number associated with model. |
| -path ../map | Path to map. |
| -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. |
| -rdf 1.2 | Calculate the radial distribution function with the given sampling (angstrom). |
| -curvature | Calculate the curvature associated with each component. |
| -settype VER | Set all component types. |
| -associate TRS,trs.pdb | Associate a component type with a file name. |
| -mass TRS,288.7 | Associate a component type with a mass. |
| -translate 12.3,95,-10.5 | Shift along a vector (x,y,z). |
| -rotate 0.5,0,5.8,45 | Rotate around a vector (x,y,z) by an angle. |
| -scale 1.5,0.8,1 | Scale around the origin. |
| -reflect 0.4,-.22,0.5 | Reflect through a mirror plane defined by the given normal. |
| -linklength 56.3 | Generate links with this maximum length. |
| -setasu D8 | Set components to within an asymmetric unit. |
| -apply C5 | Apply point group symmetry. |
| -symmetrize C5 | Symmetrize for a point group symmetry. |
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