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
- Typical usage:
<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.
- 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