| -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. |
| -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. |
| -oriflip y | Reverse the particle origins along the given axis. |
| -toview -2.5,5.5,9,45 | Transform particle orientations relative to this view. |
| -toeuler 45,30,10 | Transform particle orientations relative to these Euler angles. |
| -remove | Do not write non-selected micrographs into the parameter file. |
| -check | Check if files can be found. |
| -filenames | Delete file names of files not found. |
| -extract part | Extract views from images: mg, frame, rec, part, fil. |
| -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. |
| -verbose 7 | Verbosity of output. |
| -numberperfield 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 micrograph file paths. |
| -framepath dir/subdir | Set micrograph frames file paths. |
| -pspath dir/subdir | Set power spectrum file paths. |
| -partpath dir/subdir | Set particle file paths. |
| -filpath dir/subdir | Set filament file paths. |
| -samemgpart | Set micrograph and particle file names to be the same. |
| -Scansampling 3.6 | Set scan sampling or pixel size (um/pixel). |
| -mgpixelsize 1.2,1.15,1 | Set micrograph pixel size (angstrom/pixel, one value sets all). |
| -partpixelsize 2.3,2.2,1 | Set particle pixel size (angstrom/pixel, one value sets all). |
| -boxsize 55 | Set particle box size (default from parameter file). |
| -mgorigin 1256,1256,1 | Set micrograph origins (voxels). |
| -partorigin 215,215,1 | Set particle origins (voxels). |
| -Magnification 38500 | Set magnification. |
| -electrondose 35.5 | Set electron dose (electrons/angstrom) |
| -Defocus 1.8,0.3,-34 | Set defocus average, deviation, and astigmatism angle (um, degrees). |
| -Astigmatism 0.3,-34 | Set defocus deviation and astigmatism angle (um, degrees). |
| -Cs 2.0 | Set spherical aberration, Cs (mm). |
| -Volt 100 | Set acceleration voltage (kV). |
| -Amplitude 0.07 | Set amplitude contrast (fraction) |
| -alpha 0.15 | Set illumination half-angle (milliradians). |
| -basetype 2 | Baseline type: (default 1) |
| Type 1: Polynomial with 5 coefficients. | |
| Type 2: Double Gaussian with 5 coefficients. | |
| Type 3: EMAN style with 4 coefficients. | |
| -baseline | 1,1.5,-2.6,12.9,30,118 Baseline type and 4 or 5 coefficients: (default 1,0,0,0,0) |
| -envtype 3 | Envelope type: (default 4) |
| Type 1: Single gaussian (2 coefficients). | |
| Type 2: Single gaussian with constant (3 coefficients). | |
| Type 3: Double gaussian (4 coefficients). | |
| Type 4: Double gaussian with constant (5 coefficients). | |
| -reset defocus | Reset particle defocus to micrograph defocus. |
| -input input.star | Input master parameter file to merge in data blocks from other input files. |
| -revert part.star,15 | Replace file names with those in this file, |
| with a flag indicating: 1=mg, 2=ps, 4=rec, 8=part. | |
| -replacectf ctf.star | Replace CTF parameters with those in this file. |
| -replacepart part.star | Replace particle parameters with those in this file. |
| -validate mg.xsd | Validate XML input file(s) with this schema. |
| -ppx update | Process files in directory "ppx": |
| update: Update particle records in the parameter file. | |
| list: List existing ppx files. | |
| absent: List absent ppx 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 (no -output required). | |
| Argument: "field": field ID's are used as file names (no -output required). | |
| -dump file.txt | Dump all the particle origins and views. |