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Tutorial Tutorial is under construction

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 could be used to extract the Relion command that could be run on a local machine.


Helpful Links:

Tutorial is under construction

RELION Webpage


Program 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

--offsetrange

float

Offset search range (pix)

--offsetstep

float

Offset search step (pix)

--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

EMAN2/Programs/e2refinetorelion3d (last edited 2013-01-23 21:17:34 by StephenMurray)