= refine =
 ''This is the main refinement loop in EMAN. It has a tremendous number of options.''
== Usage ==
 refine <total iter> mask=<rad> [proc=<maxproc>] [hard=<maxpr>] [simple] [ctfc=<res in A>] [ctfcw=<SF file>] [phaseopt] [setsf=<lowpass res>[,<highpass res>[,<SF file>]] [median] [nweight] [sym=<c2,c4,etc>] [ang=<dang>] [anglist=<fule>] [maxshift=<rad>] [pad=<size>] [classkeep=<sigma coef>] [classiter=<iter>] [refmaskali] [filt3d=<lp rad>] [sep=<n>] [xfiles=<a/pix>,<mass in kd>,<ali to>] [3dit=<n it>] [3dit2=<n it>] [speed=<1-5>] [sigfilt] [euler2=<oversmp>] [tree=<2,3>] [imask=<rad>] [amask=<r>,<thr>,<n iter>] [planarmask=<thickness>] [goodbad] [slow] [refine] [shrink=<n>] [projbatches=<n>] [ca3] [classfp=<msa#>] [perturb] [usefilt] [rfp] [precen] [phasecls] [fscls] [axialfilt=<res>] [msa=<proj>] [mra2] [3dr[=<range>]] [d3s=<sigmult>] [collapse=<ang>] [dfilt] [frm2d[=<rad>,<samp>]] [classalign2log] [continue]
=== Parameters ===
 || <total iter>||Total number of iterations to be run in the current directory||
 ||mask=<rad>||Applies an outside mask at several stages of refinement||
 ||[proc=<maxproc>]||Number of proceesors to use for parallel processing||
 ||[hard=<maxpr>]||Hard limit for <a href=make3d.html>make3d</a>||
 ||[simple]||Use 'make3dsimple inorm'||
 ||[ctfc=<res in A>]||Performs CTF correction filtered to the specified resolution (see <a href=classalignall.html>classalignall</a>)||
 ||[ctfcw=<SF file>]||Performs CTF correction with Wiener filtration using a structure factor specified in a file||
 ||[phaseopt]||Experimental modification to class-averaging||
 ||[setsf=<lowpass res>[,<highpass res>[,<SF file>]]||Applies a final filter to set the radial structure factor to match the ctfcw structure factor multiplied by a gaussian filter. Filter is specified in A.||
 ||[median]||Specify this when CTF correction is NOT being performed||
 ||[nweight]||Used when start.hed contains averages, to properly weight during further averaging. This will not work in conjunction with median or ctfc/w.||
 ||[sym=<c2,c4,etc>]||Imposes symmetry on the model, omit this option for no/unknown symmetry||
 ||[ang=<dang>]||Angular step for projections (in degrees, see 'prop' in <a href=project3d.html>project3d</a>)||
 ||[anglist=<fule>]||Use Euler angles included in this file for projection||
 ||[maxshift=<rad>]||Maximum translation during image alignment||
 ||[pad=<size>]||Pads the model during Fourier reconstruction (see <a href=make3d.html>make3d</a>)||
 ||[classkeep=<sigma coef>]||Classkeep value for <a href=classalignall.html>classalignall</a>||
 ||[classiter=<iter>]||Iterations for <a href=classalignall.html>classalignall</a>||
 ||[refmaskali]||This passes the refmaskali option to classalignall if the amask option is being used, otherwise refmask is used when amask is specified.||
 ||[filt3d=<lp rad>]||Apply a lowpass filter to the model after each iteration, this occurs before 3dit||
 ||[sep=<n>]||This option is passed to <a href=classesbymra.html>classesbymra</a>||
 ||[xfiles=<a/pix>,<mass in kd>,<ali to>]||Used to generate 3d models that are easy to evaluate||
 ||[3dit=<n it>]||After constructing a model with Fourier reconstruction, this runs n iterations of real-space model 'cleansing' This option isdeprecated, suggest not using it||
 ||[3dit2=<n it>]||This is real-space refinement with a special noise elimination feature enabled. This option is deprecated, suggest not using it||
 ||[speed=<1-5>]||Speed parameter in clean3d (3dit,3dit2). Convergence rate, 1 dfl||
 ||[sigfilt]||Applies a 1-sigma real-space filter to images at various points||
 ||[euler2=<oversmp>]||Reassigns Euler angles to class averages with an optionally reduced angular increment. ie - 2 will use ang/2 (see <a href=classesrefs.html>classesrefs</a>||
 ||[tree=<2,3>]||Faster classifications for large numbers of projections (see <a href=classesbymra.html>classesbymra</a>. Limited parallel support, see text.||
 ||[imask=<rad>]||Applies an inside mask in several stages of refinement||
 ||[amask=<r>,<thr>,<n iter>]||This applies an automask between steps in a reconstruction. see automask2 in <ahref=proc3d.html>proc3d</a>. REQUIRES xfiles to be used.||
 ||[planarmask=<thickness>]||Masks the object along the z-axis with a total thickness specified in pixels.||
 ||[goodbad]||Saves good and bad class averages from 3D reconstruction. Overwrites each new iteration.||
 ||[slow]||This will use a very slow, exhaustive search, algorithm for 2D alignments. VERY SLOW||
 ||[refine]||This will do subpixel alignment of the particle translations for classification and averaging. May have a significant impact at higher resolutions.||
 ||[shrink=<n>]||Experimental, shrinks images at several points for faster runs||
 ||[projbatches=<n>]||Experimental, split the projection into n batches to minimize total memory requirement||
 ||[ca3]||Experimental. Uses classalign3 instead of classalign2||
 ||[classfp=<msa#>]||Experimental, classification using rotational/translational invariants||
 ||[perturb]||Experimental option to produce a more uniform distribution of points in 3D Fourier space.||
 ||[usefilt]||Experimental||
 ||[rfp]||Experimental, classification using rotational footprints||
 ||[precen]||Indicates that raw particles have been accurately precentered (experimental)||
 ||[phasecls]||Uses weighted mean phase error for classification (experimental)||
 ||[fscls]||Uses FSC for classification (experimental)||
 ||[axialfilt=<res>]||See proc3d, 0 provides maximal effect.||
 ||[msa=<proj>]||Experimental||
 ||[mra2]||Experimental||
 ||[3dr[=<range>]]||Experimental||
 ||[d3s=<sigmult>]||Experimental||
 ||[collapse=<ang>]||Experimental||
 ||[dfilt]||Experimental||
 ||[frm2d[=<rad>,<samp>]]||This will classify using Fast Rotational Matching 2D. rad is the maximum radius of  particles; samp is the number of angular sampling points at each radius circle||
 ||[classalign2log]||Experimental. Calls classalign2 with classalign2log option to print out particle that were used in the class average.||
 ||[continue]||If a job is killed in the middle of an iteration, this will allow it to pick up where it left off. Otherwise the last iteration will start from the beginning.||
 Typical usage:
  refine 5 ang=3 mask=28 pad=96 hard=25 classkeep=.3 classiter=8 proc=12 sym=d7 ctfc=12 sep=2 xfiles=4.2,1000,40

== Description ==