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