class-by-ort

This program is used to classify the images according to the orientations and output the class averages

class-by-ort <raw-images> <classavg.img> [classes=<num>] [list=<filename>] [plt=<plt file>] [cls] [delvoidclass] [xray=<Xray curve>] [res=<angstrom>] [outmask=<rad>] [inmask=<rad>] [tailwidth=<degree>] [tailradfactor=<num>] [verbose]

Parameters:


<raw-images>input raw particles images file
<classavg.img>output class average file
[classes=<num>]number of classes wanted, default to 3
[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
[delvoidclass]the empty class would be thrown away, default is to reassign to random position and include again
[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

Usage:

class-by-ort raw.img clsavg.img verbose

class-by-ort raw.img clsavg.img classes=100 list=class.list xray=X-ray-low-high.txt tailradfactor=1000 verbose

Description

This program is used to classify 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 class averages would be used directly for 3D reconstruction by make3d in EMAN or other single particle processing package.


EMAN Manual page, generated Tue Feb 5 15:30:08 2002