basisrefine.py

This is a highly experimental refinement procedure using a novel alignment/classification procedure

basisrefine.py <iterations> [pad=<box size>] [ang=<dang>] [proc=<nproc>] [ctfcw=<file>] [ctfc=<res>] [mask=<r>] [nbasis=<n>] [xfiles=<A/pix>,<mass>,<ali to>] [3dit=<iter>] [3dit2=<iter>] [sym=<symmetry>] [hard=<maxpr>] [automask=<r>,<thr>,<shells>] [nbasiscls=<num>] [clsbylcmp=<filt r>] [jacobi] [phicomp] [align4[=<topphi>]] [snrmult=<val>] [setsf=<lp>[,<hp>[,<sffile>] [geodc [keep=<% to keep>

Parameters:


Description

This program is still highly experimental. Contact sludtke@bcm.tmc.edu if you wish to try it.


EMAN Manual page, generated Wed Feb 18 10:51:32 2009
<iterations><iterations>
[pad=<box size>][pad=<box size>]
[ang=<dang>][ang=<dang>]
[proc=<nproc>][proc=<nproc>]
[ctfcw=<file>][ctfcw=<file>]
[ctfc=<res>][ctfc=<res>]
[mask=<r>][mask=<r>]
[nbasis=<n>][nbasis=<n>]
[xfiles=<A/pix>,<mass>,<ali to>][xfiles=<A/pix>,<mass>,<ali to>]
[3dit=<iter>][3dit=<iter>]
[3dit2=<iter>][3dit2=<iter>]
[sym=<symmetry>][sym=<symmetry>]
[hard=<maxpr>][hard=<maxpr>]
[automask=<r>,<thr>,<shells>][automask=<r>,<thr>,<shells>]
[nbasiscls=<num>][nbasiscls=<num>]
[clsbylcmp=<filt r>][clsbylcmp=<filt r>]
[jacobi][jacobi]
[phicomp][phicomp]
[align4[=<topphi>]][align4[=<topphi>]]
[snrmult=<val>][snrmult=<val>]
[setsf=<lp>[,<hp>[,<sffile>][setsf=<lp>[,<hp>[,<sffile>]]
[geodc[geodc]
[keep=<% to keep>[keep=<% to keep>]