| -all | Reset selection to all models and components before other selections. |
| -number 24,36 | Select models based on the number of components. |
| -closed order,3 | Select models based on valency (valency,) or polygon order (order,). |
| -fullerene | Select fullerene type models. |
| -select A | Select a component type. |
| -delete B | Delete a component type. |
| -merge | Merge models in different files rather than concatenate. |
| -setfom 0.8 | Set the FOM of selected components to a specific value. |
| -center | Center before all other operations. |
| -trim | Trim the components to the selected ones. |
| -average 4 | Average sequential components and delete all but one in each set. |
| -fom 0.25 | Select: FOM cutoff. |
| -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. |
| -views | Calculate views for components. |
| -invert | Invert views for selected components. |
| -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. |
| -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. |
| -symmetry C5 | Apply point group symmetry. |
| -linklength 56.3 | Generate links with this maximum length. |
| |