| -invert | Invert density for determination of the threshold. |
| -verbose 7 | Verbosity of output. |
| -componentradius 8.4 | Set radius for all components. |
| -shift 40 | Maximum shift allowed (angstrom, default infinite). |
| -resolution 50,500 | Resolution range for cross-correlation (default 0 - 1e6 angstrom). |
| -rho 0.8 | Protein density (default 0.81 Da/A3, use with -mass). |
| -mass 12.645M | Molecular mass of the particle (determines the threshold. |
| -cutoff 0.3 | Cutoff for voxels above threshold for determining occupancy (default 0.5), |
| -bins 50 | Number of bins for histogram of average intensities at the marker locations in all images. |
| -fit 2 | Number of fitted binomial distributions to the distribution of occupancy. |
| -model model.star | Input reference model of expected locations in the particle. |
| -template templ.pif | Template map for cross-correlation refinement of component locations. |
| -Mask shell.map | Binary mask to hide denisity in some regions of the map before determination of occupancy. |
| -output model.star | Model output file. |
| -split 3 | Split models into individual files: |
| Argument: 1-6: number of digits inserted before extension | |
| Argument: "id": model ID's are used as file names. | |
| -Postscript plots.ps | Postscript output file. |
| dcount -v 7 -model model_template.star -comp 15.6 -template map_template.pif -shift 55 | |
| -resol 50,500 -invert -mass 12.645M -cutoff 50 -bins 20 -fit 2 | |
| -output model_occ.star -Postscript model_occ.ps model.star | |