| -bin 3 | Bin the images before comparison. |
| -average 7 | Averaging/smoothing filter: kernel size. |
| -symmetry C5 | Find point group symmetry equivalent. |
| -fit | Fit the map to the reference. |
| -rescale -0.1,5.2 | Rescale data to average and standard deviation. |
| -verbose 7 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -origin 0.8,-10,15.7 | Set the origin (default from input image). |
| -sampling 1.5,1.5,1.5 | Dimension scaling (default 1,1,1 A/pixel). |
| -range 0.95,1.08,0.01 | Scaling range and step size (default 0.99,1.01,0.01). |
| -reference temp.map | Reference map to scale to. |
| -mask mask.mrc | Mask (must be the same size as the reference). |