= e2refinetorelion3d =


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

''e2refinetorelion3d.py'' 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: ===

[[EMAN2/Programs/e2refinetorelion3d/e2refinetorelion3dtutorial|Tutorial]]

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

----
=== Program Options: ===
||||||||I/O||
|| ||--randomizemodel||float||Optionally randomize the phases of the initial model to this resolution (in Angstroms)||
|| ||--symmgroup||string||Symmetry Group||
|| ||--symmnumber||string||Symmetry Number||
||||||||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||
|| ||--lowpass||float||Initial low-pass filter (Ang)||
|| ||--imagemaskd||float ||Diameter of the image mask||
|| ||--solventmask||string ||Location of the mask to be used||
||||||||Sampling Options||
|| ||--healpix||string||Angular Sampling Interval (Degrees)||
|| ||--auto_healpix||string||Local angular search value||
|| ||--offsetrange||float||Offset search range (pix) ||
|| ||--offsetstep||float||Offset search step (pix) ||
||||||||Run Options||
|| ||--threads||int||# of threads ||
|| ||--maxmemory||float||Maximum memory (in GB) available for each thread||
||||||||Expert Options||
|| ||--amplitudecontrast||float||Amplitude contrast value for the micrographs||
|| ||--intensitycorrection||bool||(T/F) Do intensity correction?||
|| ||--print_symmetry||bool||Print all symmetry transformation matrices and exit?||
|| ||--nearestneighbor||bool||Perform nearest-neighbor instead of linear Fourier-space interpolation||
|| ||--oversampling||int||Oversampling Order||
|| ||--limit_tilt||int||Limited tilt angle: positive for keeping side views, negative for keeping top views||
|| ||--verbosity||int||Set the level of verbosity for output ||
|| ||--onlyflipphase||bool||(T/F) Only flip phases?||
||||||||Default Options||
||-h ||--help ||bool ||show this help message and exit ||
|| ||--version ||bool ||show program's version number and exit ||