| have already been calculated and will be used for multislice simulation. | |
| -generate 10,3,50 | Generate a project, specifying number of fields, number of |
| micrographs per field and number particles per micrograph. | |
| -symmetry C5 | Generates images based on a grid in the asymmetric unit. |
| -coordinates file.pdb | Input coordinate file, generate simulated images in project. |
| -image | Generate a final image and parameter file (default not). |
| -poisson | Add poisson noise (default not). |
| -gaussian 0.2 | Add gaussian noise with the given signal-to-noise ratio. |
| -MTF 17.5 | Set the MTF decay constant (required to impose MTF). |
| -verbose 7 | Verbosity of output. |
| -translate 2.4 | Standard deviation for random translation (default 0). |
| -origin 120 | Set the particle image origin (default 50 pixels). |
| -angles 8,6 | Step sizes for theta and phi in the asymmetric unit, one value sets both. |
| Use with the -symmetry option (default 10,10). | |
| -Pixelsize 5.5 | Set the particle pixel size (default 1 angstrom/pixel). |
| -electrondose 35.5 | Set the electron dose (default 20 electrons/angstrom). |
| -Cs 2.0 | Set the spherical aberration, Cs (default 2 mm). |
| -Cc 2.0 | Set the chromatic aberration, Cc (default 2.0 mm). |
| -alpha 0.15 | Set the illumination half-angle (default 0.1 milliradians). |
| -energyspread 2e-5 | Set the effective energy spread (default 1e-5). |
| -Volt 100 | Set the acceleration voltage (default 120 kV). |
| -Amplitude 0.07 | Set the amplitude contrast (fraction, default 0.07). |
| -Defocus 0.5,3.4 | Defocus range (required to apply CTF). |
| -fieldbasename field | Field-of-view base name (default field). |
| -fieldnumber 5 | Field starting number (default 1). |
| -mgbasename mg | Micrograph base name (default mg). |
| -mgnumber 23 | Micrograph starting number (default 1). |
| -partbasename part | Particle base name (default part). |
| -partnumber 158 | Particle starting number (default 1). |
| -fieldname field | Field-of-view name (for selecting a specific field). |
| -mgname mg | Micrograph base name (for selecting a specific micrograph). |
| -partselect 132 | Particle selection for potential generation (default all). |
| -type real | Type of potential calculation (default reciprocal, other gauss). |
| -size 100,80,120 | Size of enclosing box (default based on input coordinates). |
| -thickness 20 | Slice thickness in angstrom (default 10 A). |
| -resolution 8.5 | Resolution limits (default Nyquest frequency). |
| -Bfactor 24.5 | Set the overall temperature factor (default 0 A^2). |
| -parameters param.star | Parameter file name for electron scattering curves (default atom_prop.star). |
| -Water water.pdb | Block of water to embed the molecule into (default none). |
| -output mg.star | Parameter file (use with generate option). |