| -all | Select all models for comparison. |
| -distance | Calculate a distance matrix. |
| -unknown | Select unknown models for comparison. |
| -closed order,3 | Select based on valency (valency, |
| -consensus 12.5 | Calculate a consensus model: components are considered the same if within the given distance. |
| -verbose 7 | Verbosity of output. |
| -parameters parm.star | Molecular parameter file (default atom_prop.star). |
| -reference ref.star | File with reference models. |
| -output new.star | Output model file. |
| -writereference ref.star | Reference output model file. |
| -matrix file.mat | Distance matrix. |
| -image file.map | Distance matrix as an image. |