usage: prog [options] <set name>
This program will extract the necessary parameters from an EMAN2 refinement and determine class averages using Relion 2D ML
Examples:
[-] [-] [-] [- NUMCLASSES] [-] [-] [-] [- NUMITER] [- REGPARAM]
[- PARTICLE_MASK_DIAMETER] [-] [- SOLVENTMASK] [- INPLANEANG]
[- OFFSETRANGE] [- OFFSETSTEP] [- THREADS] [- VERBOSITY] [- VOLTAGE]
[- CS] [- APIX] [- DEFOCUS] [- AMPCONT] [-] [- PPID]
[positionalargs ...]
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --numclasses | int | # of classes |
| --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? |
| --numiter | int | # of iterations to refine |
| --regparam | float | Regularization Parameter T (weights experimental data vs. prior |
| --particle_mask_diameter | float | Diameter of the soft circular image mask (in Angstroms) |
| --maskzeroes | None | (T/F) For individual particles, the area outside a circle with the radius of the particle will be set to zeros prior to taking the Fourier transform |
| --solventmask | str | Location of the mask to be used |
| --inplaneang | float | In-plane angular sampling |
| --offsetrange | float | Offset search range (pix) |
| --offsetstep | float | Offset search step (pix) |
| --threads | int | # of threads |
| --verbosity | int | Set the level of verbosity for the code |
| --voltage | int | (Expert Option) Voltage of the Microscope (kV) |
| --cs | float | (Expert Option) Spherical Aberration |
| --apix | float | (Expert Option) Angstrom per pixel |
| --defocus | float | (Expert Option) Defocus in A |
| --ampcont | float | (Expert Option) Amplitude Constrast. 10%% = .1 |
| --echo | None | Echo Relion Command to terminal only |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |
For more information go to emanwiki/EMAN2/Programs/e2refinetorelion2d.