| -setviews local | Calculate views for components. Modes: origin: current origin, |
| com: center-of-mass origin, map: map origin, local: neigbor plane. | |
| -invert | Invert views for selected components. |
| -linklength 58.4 | Reference link length to generate links (angstrom, default 1). |
| -type component | Type of element: component (default) or link. |
| -extract 80,50,30 | Extract a part of the density with the given size. |
| -build 200,250,150 | Build a new map of the given size. |
| -refine template.map | Refine the positions by cross-correlation. |
| -average 2 | Average extracted densities: averages per type (use with -extract). |
| -componenttype A,Ver | Names to assign to component types in the template file. |
| -all | Reset selection to all models and components before other selections. |
| -select #Mod1@14 | Select models and components. |
| -linkselect 2 | Link selection for building a new map (first = 1, default all). |
| -fom 0.25 | Select: FOM cutoff. |
| -verbose 7 | Verbose output. |
| -datatype u | Force writing of a new data type. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; a single value can be given). |
| -origin 0.8,-10,15.7 | Set the origin for extracted or built map |
| (origins for extract and build cannot be used together). | |
| -weigh | Weigh by contributions when building a new map (default not). |
| -separate | Separate maps for each component type (default one map). |
| Common refinement parameters: | |
| -resolution 4.5,130 | Resolution range for cross-correlation (default 0 - 1e6 angstrom). |
| -shift 2.3 | Maximum shift allowed per iteration (angstrom, default 10% map width). |
| -viewangle 1.4 | Maximum rotation angle of view vector allowed per iteration (default 0 degrees). |
| -rotationangle 3.5 | Maximum rotation angle around view vector allowed per iteration (default 0 degrees). |
| -normal | Flag to shift only along the component view vector. |
| -lateral | Flag to shift only perpendicular to the component view vector. |
| -iterations 80 | Maximum number of refining iterations (default 0 - only positional refinement). |
| -viewstep 2.5 | Angular steps in 2 view directions (default 0 degrees). |
| -rotationstep 1.3 | Angular step around view (default 0 degrees). |
| -accuracy 0.7 | Angular refinement accuracy (default 0.5 degrees). |
| -rescale -0.1,5.2 | Rescale data to average and standard deviation. |
| -parameters param.star | Input parameter file. |
| -map file.map | Input map file. |
| -mask mask.mrc | Real space mask to be applied to template and subvolumes. |
| -Mask mask.mrc | Mask for cross-correlation during refinement. |
| -output file.star | Output model parameter file. |
| -construct file.pif | Constructed map file. |
| -std file.pif | Standard deviation map file. |