| -difference 1 | Compute |difference| between measured (input) and predicted |
| orientations, 0=do not (default), 1=pred. orient. and avg | |
| |difference|, 2=#1 + individual values. | |
| -org2 cross | Get particle origins of second view by cross-correlation |
| with projections of predicted view (cross), from image | |
| files (image), or from parameter files (param, default). | |
| -selconsist | Sets selection values in unused micrographs to be consistent |
| with those in views 1 and 2. | |
| -verbose 1 | Verbosity of output. |
| -all | Include all particles (default sel>0). |
| -numberperfield 3 | Number of micrographs per field-of-view (default 1). |
| -fieldID dbgd | Set the field ID (multiple micrographs will get numbered ID's). |
| -axis 74.7 | Tilt axis angle relative to x-axis (default from parameter file). |
| -origin 50,5.3,50.4 | Set the x,y,z origin of 3D map, in pixel units. |
| -mindiff 0.05 | minimum acceptable |difference| between hand A & B |
| correlation coefficients, default = 0.050. | |
| -minfom 0.1 | min. acceptable value for FOM of correct hand, default=0. |
| -radii 5,65 | Radial limits (in pixels), default = all radii. |
| -resolution 100,17 | Resolution limits in angs. (low,high), default = 400,20. |
| -sampling 2.54 | x,y,z pixel sampling (input map and all micrographs). |
| -mgsel angle,0,-5.0 | Criterion, value for first view, value for second view |
| -mg1 index,1 | Micrograph in each set that is the first view |
| -mg2 angle,-5.0 | Micrograph in each set that is the second view |
| Options: | |
| angle,a (tilt angle) | |
| index,n (index within a series, beginning with 1) | |
| near,n (nth nearest-to-focus, beginning with 1) | |
| far,n (nth farthest-from-focus, beginning with 1) | |
| -map input.img | Reference map. |
| -output output.star | Outputs data in STAR format to output.star |
| -outprj output.img | Outputs projections to output_field#_img#_imgID.img |