classalignml

Aligns a set of images using maximum likelihood

classalignml <input file> <iterations> [ref1] [finalref] [savesteps] [saverefs] [mask=<rad>] [locfromfile] [ctfc=<res>] [ctfcw=<SF file>] [even|odd] [maxtran=<dist>] [verbose]

Parameters:


<input file>Input file, usually a cls*img file
<iterations>Number of iterative loops
[ref1]Indicates that the first image in the file is a reference
[finalref]Once the average has been generated, a final alignment to the reference is performed
[savesteps]Save the class average after each iterative step to monitor convergence
[saverefs]Write the reference image as well as the class average to the output file
[mask=<rad>]Circular mask radius for the class average
[locfromfile]Determine the output file image position from the input filename.
[ctfc=<res>]Enables CTF correction, thru resolution <res> in angstroms.
[ctfcw=<SF file>]Enables CTF correction, with Wiener filtration, requires s vs inten struct. factor file.
[even|odd]Only use the even or odd images in the input file
[maxtran=<dist>]Maximum translational shift
[verbose]Display details during optimization

Usage:

classalignml cls000.hed 8 ref1 finalref saverefs mask=32 keep=.8 locfromfile ctfc=15

Description

Generates a class-average from a set of particle images using a maximum liklihood technique. This program is still highly experimental and should not be used unless you feel like playing with the code.


EMAN Manual page, generated Wed Feb 18 10:51:32 2009