| -reconstructions | Operate on reconstruction parameters rather than micrographs. |
| -getfield field1 | Get a single field from a parameter file. |
| -getmicrograph mg1 | Get a single micrograph from a parameter file. |
| -selected | Show selected particles. |
| -histogram 80,0.01 | Histogram of magnification values of selected particles. |
| -add | Add micrograph coordinates and particle origins. |
| -extract | Extract particle views from images. |
| -write | Write particle views into images. |
| -bin 3 | Bin micrographs by given kernel size, new file names with a "_b |
| -changepixelsize 3.68 | Change the pixel size and all associated size parameters. |
| -Euler | Convert orientations from views to Euler angles. |
| -View | Convert orientations from Euler angles to views. |
| -flip y | Reverse the particle coordinates in the micrographs along the given axis. |
| -randomorigins 1.4 | Introduce random errors into origins with this standard deviation (pixels). |
| -randomviews 3.1 | Introduce random errors into views with this standard deviation (degrees). |
| -randomdefocus 0.3 | Introduce random errors into defocus with this standard deviation (um). |
| -randommag 0.1 | Introduce random errors into magnifications with this standard deviation (fraction). |
| -verbose 7 | Verbosity of output. |
| -number 3 | Number of micrographs per field-of-view (default 1). |
| -fieldID dbgd | Set the field ID (multiple micrographs will get numbered ID's). |
| -mgpath dir/subdir | Set the micrograph file paths. |
| -pspath dir/subdir | Set the power spectrum file paths. |
| -partpath dir/subdir | Set the particle file paths. |
| -filpath dir/subdir | Set the filament file paths. |
| -samemgpart | Set the micrograph and particle file names to be the same. |
| -Magnification 38500 | Set the magnification. |
| -Scansampling 3.6 | Set the scan sampling or pixel size (um/pixel). |
| -Pixelsize 5.5 | Set the pixel size (angstrom/pixel). |
| -mgorigin 1256,1256,1 | Set the micrograph origin (voxels). |
| -partorigin 215,215,1 | Set the particle origin (voxels). |
| -electrondose 35.5 | Set the electron dose (electrons/angstrom) |
| -Defocus 1.8,0.3,-34 | Set defocus average & deviation, & astigmatism angle (um, degrees). |
| -Cs 2.0 | Set the spherical aberration, Cs (mm). |
| -Volt 100 | Set the acceleration voltage (kV). |
| -Amplitude 0.07 | Set the amplitude contrast (fraction) |
| -alpha 0.15 | Set the illumination half-angle (milliradians). |
| -envelope 0.78,-215 | Envelope coefficients: Gaussian amplitude, and exponential constant (default 1,-10). |
| -baseline | 1,1.5,-2.6,12.9,30,118 Baseline type and 4 or 5 coefficients: (default 1,0,0,0,0) |
| Type 1: Polynomial with 5 coefficients. | |
| Type 2: Double Gaussian with 5 coefficients. | |
| Type 3: EMAN style with 4 coefficients. | |
| -input input.star | Input master parameter file to merge in data blocks from other input files. |
| -output output.star | Output parameter file (required any time "-split" is used to indicate the type). |
| -split 3 | Split micrograph or reconstruction data blocks into individual files: |
| Argument: 1-6: number of digits inserted before extension | |
| Argument: "id": micrograph ID's are used as file names. | |
| -dump file.txt | Dump all the particle origins and views. |