= e2refinetorelion2d =


=== Information ===
This program is normally run via the EMAN2 [[EMAN2/Programs/e2projectmanager|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.


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=== Helpful Links: ===

Tutorial is under construction

[[http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page|RELION Webpage]]

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=== 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 ||