EMAN1 Individual Programs
Description
Note: Despite the experimental tags, the 'phasecls' and 'fscls' almost always produce better results than the default linear variance classifier. Note that these options are mutually exclusive.
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/eman1/progs/eman.html eman] and following the reconstruction procedure it provides.
The tree option may not work in certian parallel configurations, such as grid configurations where the filesystem isn't cross-mounted.