| -verbose 7 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; default from input file; a single value can be given). |
| -origin 110,50,44 | Origin for rotations of the template (default taken from template image). |
| -angles 8.8,2.5,5.2 | Step size for alpha, theta and phi, one value sets all (default 45 degrees). |
| -resolution 15.6,200 | Resolution limits for cross-correlation (default 0). |
| -shiftlimit 5.2 | Radial limit to search for shift in cross-correlation map (default 1/4 of map). |
| -fullasu | Full asymmetric unit (default half). |
| -recid A435 | The 3D reconstruction ID (should correspond to that in the parameter file). |
| -image 2 | Image number in a multi-image file or particle number (default 1=first image). |
| -bin 3 | Binning of input, template and mask by given kernel size, |
| output image remains same size as input. |
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| Global and symmetric parameter: |
| -symmetry D6 | Symmetry: Point group identifier. |
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| Directional and refinement parameter: |
| -View 0.3,-0.5,0.8,33 | View to initiate search: vector {xyz} and angle. |
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| Directional parameter: |
| -limit 17.5 | Radial limit around given view (default 20 degrees). |
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| Refinement parameter: |
| -accuracy 0.3 | Accuracy (default 0.5 degrees). |
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