LEGINON ACE CORRECT DOCUMENTATION



 

  1. Experiment Name : Name of the experiment. The directory corresponding to the experiment name is shown to the left experiment name.

  2. Database Type: The two database types are Leginon1 and Leginon2 .

  3. Correction Type: The user has the option of "Phase and Amplitude" correction and "Phase only" correction.  The difference between the two is that in Phase only correction only the phase of the CTF is flipped whereas in Phase and Amplitude correction, Wiener filtering is done to correct  both phase and amplitude. If the envelope function and noise spectrum parameters are not available then phase only correction is recommended. For example if the parameters calculated from far from focus images are used   to correct near to focus images ( after adjusting for the defocus difference ), the envelope function and noise spectrum parameter estimates of far from focus images are not reliable for near to focus images. In such a case phase only correction is recommended.

  4. Extension:  The filename extension added to the corrected images. You may choose to save the corrected image with the same name as the input uncorrected image by unchecking the "Use extension" checkbox. Ensure that you are not writing to the input directory if you are not choosing an extension to avoid deletion of the original input images.

  5. File Type: The type of file you need to correct. The file selection filter should be specified in the editable textboxes. Note that if you are using far from focus image parameters to correct near to focus images , the file  filter specified in the "Other" editable box is used to load the mat files of far from focus image parameters.  For example, if filename_enr.mrc is selected for correction and the correction is done using mode 2 ( see later ) so that the corresponding far from focus images parameters are used for correction, then the parameters of filename_efar.mrc are used for correcting filename_enr.mrc if the file filters for enr is "*enr.mrc" and "Other" is "*efar.mrc". If  "*efar.mrc" is changed to "*fc.mrc" then the parameters are chosen from file filename_fc.mrc.

  6. Modes: There are three modes of correction for enr images. In mode 1 , the parameters of the CTF used for correcting is estimated from enr image itself. In mode 2  the parameters estimated for the far from focus images are used to correct near to focus images after compensating for the defocus. In mode 3, the parameters estimated for the focus images are used to correct near to focus images after compensating for the defocus. There are two modes of correction for the far from focus files. Mode 1 uses the parameters of the far from focus images while mode 3 uses the parameters of the focus images after compensating for the defocus. There is no mode 2.

  7. Directories:

    1. Space 1:  matfiles directory created by ACE while estimating the CTF parameters. 
    2. Space 2:  Directory for storing the corrected images. This directory is created if it does not exist.
  8. Message Board: Displays messages.

  9. Help: Displays this page.

  10. Process: Begins correcting the selected images.

  11. File list: Displays the list of input files to select from. Left mouse click selects the input file. To select multiple files use CTRL + click and to select all files use CTRL + a . 

  12. Console output: The output in the console can be interpretted in this way.
filename

Nominal Defocus of the file to be corrected

Nominal Defocus of the file whose matfile was  used for correction

Defocus 1 (used in correction)

Defocus  2 (used in correction)

time taken (seconds)

filename.mrc

 0.6

2.0000

0.623382

0.5817

52.53

See also documentation for aceacedemoacedemo_correct and  leginon_ace_gui .
© 2004-2005 Satya P. Mallick