This program is normally run via the EMAN2 Project Manager.

e2refinetorelion3d is run after an EMAN2 refinement has been completed. When it is run, it will take the input particle set and convert it to many normalized .mrcs files, each of which represents a single micrograph with all particles from that micrograph in it, stacked along the z-axis. It creates the "all_images.star" file which contains all of the information about the particles on a per-particle basis (CS, Defocus, Microscope Voltage, etc). It will take the input EMAN2 3D map and convert it to a Relion-style formatted map called 3DRefMap.mrc. One final thing this program does is created a directory, run01, that contains an submission script for submitting an MPI Relion job (on our clusters specifically. It will likely need to be modified to specfically address the computing environment you have). Because of the nature of Relion and of Cryo-EM itself, it is unwise to attempt to do these reconstructions on a local machine. Distributed computing works very well in these situations though the submission script can be used to extract the Relion command one could run on their local machine.

Options:

-h

--help

bool

show this help message and exit

--version

bool

show program's version number and exit

--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?

--imagemaskd

float

Diameter of the image mask

--inplaneang

float

In-plane angular sampling

--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

--numclasses

int

# of classes

--numiter

int

# of iterations to refine

--offsetrange

float

Offset search range (pix)

--offsetstep

float

Offset search step (pix)

--regparam

float

Regularization Parameter T (weights experimental data vs. prior

--solventmask

string

Location of the mask to be used

--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

--apix

float

Angstrom per pixel

--cs

float

Spherical Aberration

--defocus

float

Defocus in Angstroms

--voltage

float

Voltage of the Microscope (kV)

--echo

bool

Echo the relion command to the terminal window and exit