usage: e2make3d.py [options]
	Reconstructs 3D volumes using a set of 2D images. Euler angles are extracted from the 2D image headers and symmetry is imposed. Several reconstruction methods are available (see e2help.py reconstructors) - the fourier method is the default and recommended reconstructor.

	WARNING - the icosahedral symmetry axes are aligned differently in eman1 and eman2 - that means
	using this script to reconstruct icosahedral class averages from eman1 will give very bad results.
	Contact the developers for the simple solution.

	A simple example of usage is:

	e2make3d.py --input=classes.img --sym=c3 --output=recon.mrc --pad=128

	Because there are several default settings, this is more or less equivalent to:

	e2make3d.py --input=classes.img --sym=c3 --output=recon.mrc --pad=128 --keep=1 --recon=fourier --iter=3

	Because the padding is always done using zeroes it is critical your data (or preferably
	the edge pixels of your data) have mean zero. This will be done automatically when the data is read, but without
	any amplitude scaling. If you wish to do additional preprocessing, you can use the --preprocess
	modifier to perform additional preprocessing, eg - 

	e2make3d.py --input=classes.img --sym=c3 --output=recon.mrc --pad=128 --preprocess=normalize.edgemean

	You can add as many --preprocess arguments as you like, which are applied in
	the order in which they are specified, before padding occurs.

	If you specify a value of the keep parameter that is not one, i.e. --keep=0.9, it
	allows for the automatic exclusion of those images that agree poorly with the rest
	of the data set.

	If constructing large volumes use the --lowmem option.

Option Type Description
--output None Output reconstructed volume file name.
--input None The input projections. Project should usually have the xform.projection header attribute, which is used for slice insertion
--input_model None If the class-averages have the model_id parameter (produced by e2refinemulti.py), this will use only class-averages with the specified model_id for the reconstruction.
--tlt str An imod tlt file containing alignment angles. If specified slices will be inserted using these angles in the IMOD convention
--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.
--pad str Will zero-pad images to the specifed size (x,y) or (x,x) prior to reconstruction. If not specified no padding occurs.
--padvol str Defines the dimensions (x,y,z) or (x,x,x) of the reconstructed volume. If ommitted, implied value based on padded 2D images is used.
--outsize str Defines the dimensions (x,y,z) or (x,x,x) of the final volume written to disk, if ommitted, size will be based on unpadded input size
--recon None Reconstructor to use see e2help.py reconstructors -v. Default is fourier:mode=gauss_2
--keep float The fraction of slices to keep, based on quality scores (1.0 = use all slices). See keepsig.
--keepsig None If set, keep will be interpreted as a standard deviation coefficient instead of as a percentage.
--keepabs None If set, keep will refer to the absolute quality of the class-average, not a local quality relative to other similar sized classes.
--no_wt None This argument turns automatic weighting off causing all images to be weighted by 1. If this argument is not specified images inserted into the reconstructed volume are weighted by the number of particles that contributed to them (i.e. as in class averages), which is extracted from the image header (as the ptcl_repr attribute).
--iter int Set the number of iterations (default is 2). Iterative reconstruction improves the overall normalization of the 2D images as they are inserted into the reconstructed volume, and allows for the exclusion of the poorer quality images.
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness
--nofilecheck None Turns file checking off in the check functionality - used by e2refine.py.
--check, -c None Performs a command line argument check only.
--lowmem None Causes images to be loaded as needed to reduce memory usage at the cost of time.
--preprocess str preprocessor to be applied to the projections prior to 3D insertion. There can be more than one preprocessor and they are applied in the order in which they are specifed. Applied before padding occurs. See e2help.py processors for a complete list of available processors.
--setsf str Force the structure factor to match a 'known' curve prior to postprocessing (<filename>, auto or none). default=none
--postprocess str postprocessor to be applied to the 3D volume once the reconstruction is completed. There can be more than one postprocessor, and they are applied in the order in which they are specified. See e2help.py processors for a complete list of available processors.
--apix float A/pix value for output, overrides automatic values
--start str This is a starting model for FFT reconstruction
--startweight float This is the starting model weight
--ppid int Set the PID of the parent process, used for cross platform PPID

For more information go to emanwiki/EMAN2/Programs/e2make3d.