| -translate 0,-50,22 | Translate (angstrom). |
| -rotate 0.5,0,5.8,45 | Rotate around a vector (x,y,z) by an angle. |
| -select CA | Atom selection (default all). |
| -apply C5 | Apply point group symmetry. |
| -find C5 | Find standard orientation for this point group symmetry. |
| -pdbsymmetry | Read SMTRY matrices from a PDB file and apply them. |
| -pdbbiomt | Read BIOMT matrices from a PDB file and apply them. |
| -rename D | Rename molecules from the given letter. |
| -show | Show operational symmetry matrices. |
| -verbose 7 | Verbosity of output. |
| -origin 10,-10,20 | Origin for rotation (default 0,0,0, can be "center" for COM). |
| -reference 0,1.5,-0.2,35 | Reference symmetry axis and rotation angle (default 0,0,1,0). |
| -distance 3.5 | Distance between overlapping atoms allowed (default 3 angstrom, use with -apply). |
| -parameters parm.star | Atomic properties parameter file (default atom_prop.star). |
| -similarity sim.star | Residue similarity matrix for finding orientation (default blosum62.star). |