| -rename D | Rename molecules from the given letter. |
| -renumber 52 | Renumber residues from the given number. |
| -select CA | Atom selection (default all). |
| -elements | Use elements as identifiers for atom types. |
| -split | Split molecule groups, output multiple numbered files. |
| -slices 23.7 | Split coordinates into slices of this thickness, output multiple numbered files. |
| -translate 0,-50,22 | Translate (angstrom). |
| -trim 200,230,180 | Trim to new box size (use with -translate). |
| -noH | Remove all hydrogens. |
| -SS 2.2 | Add disulfide bonds within the given separation. |
| -nobonds | Remove all bond specifications. |
| -bonds 2.1 | Add bonds between atoms closer than the given distance. |
| -pseudobonds 3 | Add pseudo-atoms on bonds given the number per bond. |
| -random 1.2 | Add a random displacement to each coordinate within a maximum (angstrom). |
| -B 23.4 | Add a random displacement to each coordinate based on a B-factor (angstrom^2). |
| -prune | Remove overlapping molecules. |
| -untangle 3.5,0.2 | Eliminate overlaps by moving molecules apart (sampling and damping factor). |
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