| -reconstructions | Operate on reconstruction parameters rather than micrographs. |
| -all | Reset selection to all particles before other selections. |
| -find 20 | Finds the centers of the particle images (iterations). |
| -shift | Center the actual particle images (new images with "_cen" in names). |
| -align | Output aligned particle images (new images with "_aln" in names). |
| -rescale -0.1,5.2 | Rescale particle images to average and standard deviation. |
| -settilt -30,45 | Set micrograph tilt, axis and particle defocus. |
| -calctilt | Calculate micrograph tilt parameters from particle defocus. |
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