Refine command options

The refine command is at the heart of using EMAN1 for single particle reconstructions, and it has many options, some of which can produce truly awful results, so it is important not to simply go into the process blindly. This is an overview of the various parameters:

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>] [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>] [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] [continue]

Normally used



EMAN1/FAQ/Refine (last edited 2009-12-26 17:41:44 by SteveLudtke)