| -invert 10,-5.3,2.6 | Invert through a point. |
| -translate 0,-50,22 | Translate (angstrom). |
| -scale 2,1.5,2.2 | Scale the coordinates. |
| -rotate 0.5,0,5.8,45 | Rotate around a vector (x,y,z) by an angle. |
| -toview 0.3,0.5,0.8,33 | Rotate to view: vector {xyz} and angle (default 0,0,1,0). |
| -fromview 0.3,0.5,0.8,33 | Rotate from view: vector {xyz} and angle (default 0,0,1,0). |
| -radius 41.8 | Force all coordinates to this radius (default not). |
| -rename D | Rename molecules from the given letter. |
| -renumber 52 | Renumber residues from the given number. |
| -occupancy 27,99,3 | Set an occupancy range (res1,res2) to a value. |
| -box 15,66,54 | Consolidate structure within box (0,0,0 means no change). |
| -wrap 15,66,54 | Pack coordinates within periodic box. |
| -Bfactor | Analyze B-factors. |
| -Sequence | Output sequence as string of letters. |
| -Mass | Calculate the total molecular weight and volume. |
| -Volume 1 | Calculate the Van der Waals volume, wrapping flag (default 0). |
| -Composition | Calculate the composition. |
| -Center | Calculate the center of mass. |
| -Translate | Translate the coordinate set to the center of mass. |
| -Place -43.2,33,0 | Place the center-of-mass at the given coordinates. |
| -Axes | Calculate the orthogonal axes. |
| -Sphericity 1.5 | Calculate the sphericity with the given angular sampling. |
| -Radialdensity 0.05,6,1 | Calculate the radial density function at a given sampling |
| and distance cutoff (angstrom) with optional wrapping. |
| |