I/O

--numclasses

int

# of classes

CTF Options

--ctfcorrect

bool

(T/F)Do CTF Correction?

--dataphaseflipped

bool

(T/F)Has the data been phase flipped already?

--ignoretofirstpeak

bool

(T/F)Ignore CTF's until the first peak?

Optimisation Options

--numiter

int

# of iterations to refine

--regparam

float

Regularization Parameter T (weights experimental data vs. prior

--imagemaskd

float

Diameter of the image mask

--maskzeroes

bool

(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

string

Location of the mask to be used

Sampling Options

--inplaneang

float

In-plane angular sampling

--offsetrange

float

Offset search range (pix)

--offsetstep

float

Offset search step (pix)

Running Options

--threads

int

# of threads

--verbosity

int

Set the level of verbosity for output

Expert Options: used only if this information is not present in the previous EMAN2 reconstruction

--voltage

float

Voltage of the Microscope (kV)

--cs

float

Spherical Aberration

--apix

float

Angstrom per pixel

--defocus

float

Defocus in Angstroms

Default Options

-h

--help

bool

show this help message and exit

--version

bool

show program's version number and exit

--echo

bool

Echo the relion command to the terminal window and exit