| -seed 1.3,-95,75 | Transfers seed markers from first to second series, |
| using the angular increment to test for rotation angle, | |
| within the angular limits (default -180,180). | |
| -refine | Refines markers from the second series after transfer. |
| -transform | Calculates the correct micrograph transformations for the 2nd series. |
| -deselect 5-9,33 | Deselect markers by id from all micrographs and models. |
| -zcompare | Compare Z coordinates of the first and second series. |
| -verbose 7 | Verbosity of output. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; a single value can be given). |
| -resolution 900,300 | High and low resolution limits for cross-correlation (default 0.1,1000 angstrom). |
| -shiftlimit 155.5 | Limit on micrograph shift search in pixels (default 20% of micrograph width). |
| -output file.star | Output parameter file for 2nd series. |
| -Postscript out.ps | Postscript output with Z coordinate error plots. |
| -bild out.bld | BILD output with fitted marker models. |