version

bool

Show program's version number and exit

h, help

bool

Show help

c, check

bool

Checks the contents of the current directory to verify that e2refine.py will work

v, verbose

int

Toggle verbose mode - prints extra infromation to the command line while executing

input

string

The input image stack of 2D particles

iter

int

The number of refinement iterations

lowmem

boolean

A low memory flag used to indicate memory should be used as sparsely as possible

model

string

The seeding 3D model

path

string

The directory where output will be stored

sym

string

The symmetry being output 3D models and the limit the range of generated projections

orientgen

string:args

The OrientationGenerator and parameters used for generation orientations in the asymmetric unit of the 3D model

projector

string:args

The projector used for generating projections

shrink

int

The shrink factor applied to particles prior to generation of the similarity matrix (e2simmx.py)

simalign

string:args

The main aligner used during similarity matrix generation

simaligncmp

string:args

The comparator used by the main aligner during similarity matrix generation

simcmp

string:args

The comparator used to generate the final score which is stored in the similarity matrix

simralign

string:args

The refinement aligner used during similarity matrix generation

simraligncmp

string:args

The comparator used by the refine align in similarity matrix generation

twostage

bool

Performs particle classification in two stages, first coarsely, then locally. Generally gives 5-10x speedups with no accuracy penalty. See EMAN2/Programs/e2simmx2stage for details.

sep

int

The number of classes each particles can be associated with

classalign

string:args

The aligner used for alignment during iterative class averaging

classaligncmp

string:args

Comparator used by the main aligner during iterative class averaging

classaverager

string::args

Averager used for averaging the images in each class

classcmp

string:args

The main comparator used to quality and exclude bad particles in iterative class averaging

classiter

int

The number of class averaging iterations

classkeep

float

The keep threshold used for excluding bad particles in iterative class averaging

classnormproc

string:args

The normalization processor used in class averaging

classralign

string:args

The refinement aligner used in iterative class averagin

classraligncmp

string:args

The comparator used by the refinement aligner in iterative class averaging

m3diter

int

The number of iterations used my make3d when performing the Fourier inversion method of 3D reconstruction

m3dkeep

float

The keep threshold used by e2make3d for the purpose of slice exclusion during 3D reconstruction

m3dpreprocess

string:args

The normalization processor applied prior to slice insertion during 3D reconstruction

pad

int

The amount of padding used by the Fourier inversion 3D reconstruction technique

recon

string:args

The reconstructor used for performing 3D reconstruction

mass

float

The estimated mass of the particle in kilodalton that, along with the apix argument, is used to run the normalize.bymass processor immediately after 3D reconstruction

apix

float

The physical distance represented by a single pixel. This parameter, along with the mass argument, is used to run the normalize.bymass processor immediately after 3D reconstruction. The apix argument is also used for generating the x-axis of the automatically generated convergence plots.

automask3d

float,int,int,int

The threshold, radius, nshells and nshellsgauss parameters, respectively, of the mask.auto3d processor, which is applied directly after the application of the normalize.bymass processor.