usage: prog [options] <set name> <reference map name>
This program will extract the necessary parameters from an EMAN2 refinement and
Examples:
[-] [-] [-] [- RANDOMIZEMODEL] [-] [- SYMMGROUP] [- SYMMNUMBER] [-] [-]
[-] [- LOWPASS] [- PARTICLE_MASK_DIAMETER] [- SOLVENTMASK] [- HEALPIX]
[- AUTO_HEALPIX] [- OFFSETRANGE] [- OFFSETSTEP] [- THREADS]
[- MAXMEMORY] [- AMPLITUDECONTRAST] [-] [-] [-] [- PAD] [- LIMIT_TILT]
[- VERBOSE] [-] [- PPID]
[positionalargs ...]
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --randomizemodel | None | Optionally randomize the phases of the initial model to this resolution (in Angstroms) |
| --greyscale | None | Is the reference map in greyscale? |
| --symmgroup | None | Symmetry group |
| --symmnumber | int | Symmetry number |
| --ctfcorrect | None | (T/F)Do CTF Correction? |
| --dataphaseflipped | None | (T/F)Has the data been phase flipped already? |
| --ignoretofirstpeak | None | (T/F)Ignore CTF's until the first peak? |
| --lowpass | float | Initial low-pass filter for the reference map (Ang) |
| --particle_mask_diameter | float | Diameter of the soft spherical image mask in angstroms |
| --solventmask | str | Location of the mask to be used |
| --healpix | str | Angular Sampling Interval (Degrees) |
| --auto_healpix | str | Local angular search value |
| --offsetrange | float | Offset search range (pix) |
| --offsetstep | float | Offset search step (pix) |
| --threads | int | # of threads |
| --maxmemory | float | Maximum memory (in GB) available for each thread |
| --amplitudecontrast | float | Amplitude Contrast value for the micrographs |
| --intensitycorrection | None | (T/F)Perform intensity-scale corrections on image groups? |
| --print_symmetry | None | Print all symmetry transformation matrices, and exit |
| --nearest_neighbor | None | Perform nearest-neighbor instead of linear Fourier-space interpolation |
| --pad | int | Padding factor |
| --limit_tilt | int | Limited tilt angle: positive for keeping side views, negative for keeping top views |
| --verbose | int | Set the level of verbosity for the code |
| --onlyflipphase | None | (T/F)Only flip phases? |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |
For more information go to emanwiki/EMAN2/Programs/e2refinetorelion3d.