e2refinetorelion2d

Information

This program is normally run via the EMAN2 Project Manager.

e2refinetorelion2d.py is typically run after particles have been boxed and particle sets have been created. It can be used as another way to generate class averages in a reference-free manner. When it is run, it will launch Relion to generate class averages with the specified number of classes.


Helpful Links:

Tutorial is under construction

RELION Webpage


Program Options:

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

EMAN2/Programs/e2refinetorelion2d (last edited 2013-01-23 21:17:53 by StephenMurray)