refine

This is the main refinement loop in EMAN. It has a tremendous number of options.

refine <total iter> [proc=<min proc>,<maxproc>] [hard=<maxpr>] [ctfc=<res in A>] [ctfcw=<SF file>] [median] [sym=<c2,c4,etc>] [ang=<dang>] [mask=<rad>] [maxshift=<rad>] [pad=<size>] [classkeep=<sigma coef>] [classiter=<iter>] [filt3d=<lp rad>] [sep=<n>] [xfiles=<a/pix>,<mass in kd>,<ali to>] [3dit=<n it>] [3dit2=<n it>] [sigfilt] [euler2=<oversmp>] [tree=<2,3>] [imask=<rad>] [amask=<r>,<thr>,<n iter>] [goodbad] [slow] [shrink=<n>] [ca3] [classfp=<msa#>] [usefilt] [rfp] [precen] [msa=<proj>] [mra2] [3dr[=<range>]] [d3s=<sigmult>] [collapse=<ang>]

Parameters:


<total iter>Total number of iterations to be run in the current directory
[proc=<min proc>,<maxproc>]Number of proceesors to use for parallel processing
[hard=<maxpr>]Hard limit for <a href=make3d.html>make3d</a>
[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
[median]Specify this when CTF correction is NOT being performed
[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>)
[mask=<rad>]Applies an outside mask in several stages of refinement
[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>
[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'
[3dit2=<n it>]This is real-space refinement with a special noise elimination feature enabled.
[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>
[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 <a href=proc3d.html>proc3d</a>. REQUIRES xfiles to be used.
[goodbad]Save files with good and bad particles, for diagnostic purposes
[slow]This will use a very slow, exhaustive search, algorithm for 2D alignments. VERY SLOW
[shrink=<n>]Experimental, shrinks images at several points for faster runs
[ca3]Experimental. Uses classalign3 instead of classalign2
[classfp=<msa#>]Experimental, classification using rotational/translational invariants
[usefilt]Experimental
[rfp]Experimental, classification using rotational footprints
[precen]Indicates that raw particles have been accurately precentered (experimental)
[msa=<proj>]Experimental
[mra2]Experimental
[3dr[=<range>]]Experimental
[d3s=<sigmult>]Experimental
[collapse=<ang>]Experimental

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 tree=3 3dit=5

Description

This is the main refinement command in EMAN. You should have your starting images in 'start.img' and your initial 3D model in threed.0a.mrc. The 'refine' command will then refine this model iteratively. Note that the 'total number of iterations' specifies the number of iterations the program will finish with. If 5 iterations have been run, then 'refine 8 ...' is run, the program will pick up after 5 iterations and run only 3 more cycles. If you want to start over again from the first iteration, you must remove all of the 'threed.?.mrc' files (except for 0a) and all of the 'classes.?.mrc' files.

Most of the options are simply passed through to other programs. Typical options for this program can be determined by running eman and following the reconstruction procedure it provides.


EMAN Manual page, generated Tue Oct 8 21:38:48 2002