<raw-images> | input raw particles images file |
<groupavg.img> | output class average file |
[step=<degree>] | angular stepsize, default to 3 degree |
[list=<filename>] | output file for the classes information |
[plt=<plt file>] | the plt format orientation file, for IMAGIC true3d reconstruction |
[cls] | to output raw particles grouped into corresponding classes, files are cls###.img/hed |
[xray=<Xray curve>] | file constaining the x-ray solution scattering curve |
[res=<angstrom>] | resolution cutoff when applying CTF correction, ignored if [xray=<Xray curve>] is set, default to 20A |
[outmask=<rad>] | largest mask radius(pixels), default to 128 |
[inmask=<rad>] | smallest mask radius(pixels), default to 100 |
[tailwidth=<degree>] | angular width of the tail, default to 45degree |
[tailradfactor=<num>] | control the shape of tail mask, the larger the less cone like, default to 1 |
[verbose] | set to output some intermediate information |
avg-by-ort raw.img groupavg.img verbose
avg-by-ort raw.img groupavg.img step=3 list=class.list xray=X-ray-low-high.txt tailradfactor=1000 verbose
This program is used to group the raw particle images after the orientations are assigned (in constrast the opposite order for standard single particle processing. This is mainly for the hybrid 3D processing of tailed P22 particles. The output group averages would be used directly for 3D reconstruction by make3d in EMAN or other single particle processing package.