usage: prog [options] 
	This program is designed to generate a reconstruction via the random conical tilt technique.
	Starting from a tilted and untilted dataset. Thce program interfaces with e2refine2d.py to 
	find the azimuthal angles from the untilited dataset and e2make3d.py to make the 3D model
	from the untilted dataset combined with the azimuthal angles and stage tilt. A model is made
	foreach e2refine2d.py class(used for alignment)

Option Type Description
--version None show program's version number and exit
--path str Path for the rct reconstruction, default=auto
--untiltdata str Name of the tilted dataset
--tiltdata str Name of the tilted dataset
--classavg str Name of classavg file created by e2refine2d.py
--stagetilt float Amount of tiliting of the cryo stage, default=0, get the stage tilt from particle attributes. Only possible if e2RCTboxer was used for particle picking
--careject str class averages to reject, default=None
--minproj int Minimum number of projections/images in a class average, for a class average to be used for a reconstruction, default=auto
--align None Switch on image alignment. This is only translational alignment for the tilted images, and uses a iterative method similar to EMAN1 centalignint
--tiltaxis None Do a tiltaxis correction(Takes into account variations in tilt axis from micrograph to micrograph. Only possible if e2RCTboxer was used for particle picking
--maxshift int Maximun amount to shift the images during alignment
--process str process RCT recons. Usually used to filter RCTS
--avgrcts None If set recons from each CA will be alinged and averaged.
--reference str Reference used to align RCT recons to, needs to be aligned to symetry axis is --sym is specified
--sym None Set the symmetry; if no value is given then the model is assumed to have no symmetry.\nChoices are: i, c, d, tet, icos, or oct.
--cuda None Use CUDA for the alignment step.
--aligngran float Fineness of global search in e2align3d.py, default=10.0
--weightrecons None Weight the reconstruction by particle numbers.
--ppid int Set the PID of the parent process, used for cross platform PPID
--verbose int verbose level [0-9], higher number means higher level of verboseness

For more information go to emanwiki/EMAN2/Programs/e2rct.