| -verbose 7 | Verbosity of output. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; a single value can be given). |
| -bbox 0,82.5,50,50,80,50 | Bounding box center and size (default from coordinates or map). |
| -wrap | Wrap around (periodic boundaries). |
| -resolution 20 | Resolution limit (angstrom). |
| -iterations 60 | Maximum number of iterations (default 1). |
| -Kbond 150 | Bond strength (default 0). |
| -Kangle 4 | Angle strength (default 0). |
| -Kvdw 0.1 | Van der Waals strength (default 0). |
| -Kelectrostatic 0.4 | Electrostatic strength (default 0). |
| -Kseparation 0.02 | Separation energy constant (default 0). |
| -Kmap 1.5 | Map energy constant (default 1 if -Map option is used). |
| -separation 4.5 | Separation distance for overlap calculation (default 4 A). |
| -cutoff 7.8 | Distance cutoff for non-bonded forces (default 5 A). |
| -beta 12 | Inverse of mean energy per atom and degree of freedom (default 10). |
| -angle 1.5 | Maximum angular increment per iteration (default 1 degree). |
| -shift 3.1 | Maximum shift per iteration (default 1 angstrom). |
| -bondsteps 5 | Number of steps along a bond for map fitting (default none). |
| -location 12,5.3,6 | Location of harmonic force to apply to center-of-mass. |
| -Klocation 16.8,0.2 | Magnitude of harmonic force and decay constant. |
| -SS 2.05 | Set disulphide reference bond length. |
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