| -create 12 | Create an alpha helix of a given length. |
| -helix 213,236 | Set residues to a helix (all molecules). |
| -find | Find a helix center and orientation (only for a single helix). |
| -set | Set a helix to the standard orientation (only for a single helix). |
| -consolidate | Consolidate a set of helices to eliminate redundancy. |
| -verbose 7 | Verbosity of output. |