usage: e2refine_easy.py [options]

	This is the primary single particle refinement program in EMAN2.1+. It replaces earlier programs such as e2refine.py
and e2refine_evenodd.py. Major features of this program:

 * While a range of command-line options still exist. You should not normally specify more than a few basic requirements. The rest will be auto-selected for you.
 * This program will split your data in half and automatically refine the halves independently to produce a gold standard resolution curve for every step in the refinement.
 * An HTML report file will be generated as this program runs, telling you exactly what it decided to do and why, as well as giving information about runtime, etc while the job is still running.
 * The gold standard FSC also permits us to automatically filter the structure at each refinement step. The resolution you specify is a target, NOT the filter resolution.
 * If --inputavg is specified to use a different stack for alignment and averaging, both stacks must have the same box size and sampling
 * Many of the 'advanced' options are hidden in the e2projectmanager.py GUI, because most users should not need to specify them.

To run this program, you would normally specify only the following options:
  --model=<starting map to seed refinement>
  --input=<lst file referencing phase-flipped particles in HDF format used for alignment>
  --inputavg=<optional lst file with particles to be reconstructed, if not specified --input used>
  --startfrom=<path to existing refine_xx directory to continue from>

  --targetres=<in A>     Resolution to target in Angstroms in this refinement run. Do not be overoptimistic !
                         Generally begin with something conservative like 25, then use --startfrom and reduce
                         to ~12, only after that try for high (3-8 A). Data permitting, of course. Low resolution
                         attempts will run MUCH faster due to more efficient parameters.
  --speed=<1-7>          Default=5. Larger values will run faster but slightly decrease measured resolution. 7 may
                         be useful for initial refinement runs. 5 is good for routine refinement. You may consider 1
                         when all other possibilities are exhausted and you are ready to push for a final published map.
                         This option modifies several parameters, including the angular step, sep= and even the
                         specific alignment and similarity metric options. The resolution difference between 1 and 7 is
                         generally no more than 10%.
  --sym=<symmetry>       Symmetry to enforce during refinement (Cn, Dn, icos, oct, cub).
                         Default=c1 (no symmetry)
  --mass=<in kDa>        Putative mass of object in kDa, but as desired volume varies with resolution
                         actual number may vary by as much a ~2x from the true value. The goal is to
                         have a good isosurface in the final map with a threshold of 1.0.
  --parallel=<par spec>  While not strictly required, without this option the refinement will run on a single CPU
                         and you will likely wait a very long time. To use more than one core on a single computer,
                         just say thread:N (eg - thread:4). For other options, like MPI, see:
                         http://blake.bcm.edu/emanwiki/EMAN2/Parallel for details.
  --threads=<ncpu>       For some algorithms, processing in parallel over the network (MPI) works poorly.
                         Running on multiple processors on a single machine may still be worthwhile. If you specify this
                         option, in specific cases it will replace your specified --parallel option. Specify
                         the number of cores that can be used on a single machine.

  --tophat=<local,global>  Some other packages (Relion) apply a tophat filter to the final map which helps exaggerate
                           the apperance of sidechains at near atomic resolution, but can also cause some artifacts.
                           'local' will produce a similar effect in the final map (but probably should be limited to
                           subnanometer resolution.
                           'global' uses a local resolution computation to locally filter the map. This can actually
                           lead to better resolution (in the good domains). While new, this may be a good idea to
                           use in pretty much all refinements.
                           To disable tophat, don't specify it, or specify "none".
  --nogoldfinal            Normally used in conjunction with tophat=local. During a refinement, the even/odd maps may
                           diverge slightly if there is any structural variability in the maps. This will disable 
                           gold-standard refinement mode in the final iteration to produce a more accurate filter.
                           This may cause the FSC curve to be somewhat exxagerated as well, though.
  --apix=<A/pix>           The value will normally come from the particle data if present (set to -1). You can 
                           override if necessary.
  --sep=<classes/ptcl>     each particle will be put into N classes. Improves contrast at cost of rotational blur.
  --classkeep=<frac>       fraction of particles to use in final average. Default 90%. Should be >50%
  --m3dkeep=<frac>         fraction of class-averages to use in 3-D map. Default=auto
  --classautomask          applies an automask when aligning particles for improved alignment
  --m3dpostprocess         <name>:<parm>=<value>:...  An arbitrary processor
                           (e2help.py processors -v2) to apply to the 3-D map after each
                           iteration. Default=none
  --path=<path>            Normally the new directory will be named automatically. If you prefer your own convention
                           you can override, but it may cause minor GUI problems if you break the standard naming

Since many parameters are now selected automatically, if you are curious exactly what the differences are between any
two refinements, on Linux/Mac, you can run, for example, diff refine_01/0_refine_parms.json refine_02/0_refine_parms.json
to compare exactly what changed between the two runs.

  There are numerous additional options based on the original e2refine.py command. These options are not available from
the graphical interface, as it is generally best to let e2refine_easy pick these values for you. Normally you should
not need to specify any of the following other than the ones already listed above:

Option Type Description
--version None show program's version number and exit
--input str Image stack containing phase-flipped particles used for alignment
--inputavg str Optional file containing alternate version of the particles to use for reconstruction after alignment
--model str The map to use as a starting point for refinement
--startfrom str Path to an existing refine_xx directory to continue refining from. Alternative to --input and --model.
--targetres float Target resolution in A of this refinement run. Usually works best in at least two steps (low/medium resolution, then final resolution) when starting with a poor starting model. Usually 3-4 iterations is sufficient.
--speed int (1-7) Balances speed vs precision. Larger values sacrifice a bit of potential resolution for significant speed increases. Set to 1 when really pushing resolution. Set to 7 for initial refinements. default=5
--sym None Specify symmetry - choices are: c<n>, d<n>, tet, oct, icos.
--breaksym None If selected, reconstruction will be asymmetric with sym= specifying a known pseudosymmetry, not an imposed symmetry.
--focused None Highly experimental, and under development! Specify a 3-D mask. Not used for coarse alignment, but only for final 'fine tuning' and symmetrizing. With symmetry also use breaksym.
--tophat str 'local', 'localwiener' or 'global'. Instead of imposing a final overall Wiener filter, use a tophat filter (global similar to Relion). local is a local tophat filter, localwiener is a localized Wiener filter
--nogoldfinal None If selected, the final iteration will turn off gold-standard behavior and both halves will be refined from the same model. Normally used with --tophat=local.
--treeclassify None Classify using a binary tree.
--norandomphase None Suppress independent phase randomization of input map. Only appropriate if input map has been preprocessed in some suitable fashion.
--m3dold None Use the traditional e2make3d program instead of the new e2make3dpar program
--iter int The total number of refinement iterations to perform. Default=auto
--mass float The ~mass of the particle in kilodaltons, used to run normalize.bymass. Due to resolution effects, not always the true mass.
--invar None Will use invariants for orientation determination, set invariant type in project (EXPERIMENTAL).
--mirror None Default for non bispectrum refinement is to handle mirrored projections by permitting flips in 2-D alignment. This will force the normal refinement to make explict mirrored projections
--apix float The angstrom per pixel of the input particles. Normally set to 0, which will read the value from the header of the input file
--sep int The number of classes each particle can contribute towards (normally 1). Increasing will improve SNR, but produce rotational blurring.
--classkeep float The fraction of particles to keep in each class, based on the similarity score. (default=0.9 -> 90%%)
--classautomask None This will apply an automask to the class-average during iterative alignment for better accuracy. The final class averages are unmasked.
--prethreshold None Applies a threshold to the volume just before generating projections. A sort of aggressive solvent flattening for the reference.
--eulerrefine None Refines Euler angles of class-averages before reconstruction
--m3dkeep float The fraction of slices to keep in e2make3d.py. Default=0.8 -> 80%%
--m3dpostprocess str Default=none. An arbitrary post-processor to run after all other automatic processing. Maps are autofiltered, so a low-pass filter should not normally be used here.
--parallel, -P str Run in parallel, specify type:<option>=<value>:<option>=<value>. See http://blake.bcm.edu/emanwiki/EMAN2/Parallel
--threads int Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful
--path str The name of a directory where results are placed. Default = create new refine_xx
--compressbits int Bits of precision to keep in class-averages and 3-D volumes, 0->losless, default=10 (3 decimal digits of precision)
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness
--automaskexpand int Default=boxsize/20. Specify number of voxels to expand mask before soft edge. Use this if low density peripheral features are cut off by the mask.
--automask3d str Default=auto. Specify as a processor, eg - mask.auto3d:threshold=1.1:radius=30:nshells=5:nshellsgauss=5.
--automask3d2 str Default=none. If specified, this mask will be multiplied by the result of the first mask, eg - using mask.soft to mask out the center of a virus.
--projector None Default=standard. Projector to use with parameters.
--orientgen str Default=auto. Orientation generator for projections, eg - eman:delta=5.0:inc_mirror=0:perturb=1
--simalign str Default=auto. The name of an 'aligner' to use prior to comparing the images
--simaligncmp str Default=auto. Name of the aligner along with its construction arguments
--simralign str Default=auto. The name and parameters of the second stage aligner which refines the results of the first alignment
--simraligncmp str Default=auto. The name and parameters of the comparitor used by the second stage aligner.
--simcmp str Default=auto. The name of a 'cmp' to be used in comparing the aligned images
--simmask str Default=auto. A file containing a single 0/1 image to apply as a mask before comparison but after alignment
--shrink int Default=auto. Optionally shrink the input particles by an integer amount prior to computing similarity scores. For speed purposes. 0 -> no shrinking
--shrinks1 int The level of shrinking to apply in the first stage of the two-stage classification process. Default=0 (autoselect)
--prefilt None Default=auto. Filter each reference (c) to match the power spectrum of each particle (r) before alignment and comparison. Applies both to classification and class-averaging.
--prectf None Default=auto. Filter each reference (c) to match the power spectrum of each particle (r) before alignment and comparison. Applies both to classification and class-averaging.
--cmpdiff None Used only in binary tree classification. Use a mask that focus on the difference of two children.
--treeincomplete int Used only in binary tree classification. Incompleteness of the tree on each level.Default=0
--classkeepsig None Change the keep ('--keep') criterion from fraction-based to sigma-based.
--classiter int Default=auto. The number of iterations to perform.
--classalign str Default=auto. If doing more than one iteration, this is the name and parameters of the 'aligner' used to align particles to the previous class average.
--classaligncmp str Default=auto. This is the name and parameters of the comparitor used by the fist stage aligner.
--classralign str Default=auto. The second stage aligner which refines the results of the first alignment in class averaging.
--classraligncmp str Default=auto. The comparitor used by the second stage aligner in class averageing.
--classaverager str Default=auto. The averager used to generate the class averages. Default is auto.
--classcmp str Default=auto. The name and parameters of the comparitor used to generate similarity scores, when class averaging.
--classnormproc str Default=auto. Normalization applied during class averaging
--classrefsf None Use the setsfref option in class averaging. This matches the filtration of the class-averages to the projections for easier comparison. Disabled when ampcorrect=flatten is used.
--pad int Default=auto. To reduce Fourier artifacts, the model is typically padded by ~25 percent - only applies to Fourier reconstruction
--recon None Default=auto. Reconstructor to use see e2help.py reconstructors -v
--m3dkeepsig None Default=auto. The standard deviation alternative to the --m3dkeep argument
--m3dpreprocess str Default=auto. Normalization processor applied before 3D reconstruction
--ampcorrect None Will perform amplitude correction via the specified method. 'flatten' requires a target resolution better than 8 angstroms (experimental). 'none' will disable amplitude correction (experimental).
--lowmem None Default=auto. Make limited use of memory when possible - useful on lower end machines
--ppid int Set the PID of the parent process, used for cross platform PPID

For more information go to emanwiki/EMAN2/Programs/e2refine_easy.