ACEDEMO CORRECT DOCUMENTATION


 

  1. Directories:

    1. Space 1:  Directory of input mrc files to be corrected.
    2. Space 2:  Directory of matfiles generated by ACE.
    3. Space 3:  Directory to store the output mrc files. 
  2. 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.

  3. 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.

  4. File: 

    1. Input File Extension: The extension which distinguishes the input files.
    2. MAT file extension:  The extension which distinguishes the matfiles. Since, it is sometimes difficult to estimate the CTF for near to focus (NTF) images directly, it can be estimated using the Far From Focus (FFF) images (or from carbon images near the location of the Near to Focus images ) and then applied to the NTF images by knowing the defocus offset.
  5. Defocus offset: If the CTF correction needs to be applied to the NTF images based on the CTF estimated for FFF  images (or carbon images), the defocus offset needs to be specified. The defocus offset is the difference between the nominal defocus set for the NTF images and that set for the FFF (or carbon) images. 
  6. Message Board: Displays messages.

  7. Help: Displays this page.

  8. Process: Begins correcting the selected images.

  9. 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 . 

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

Defocus 1 (used in correction)

Defocus  2 (used in correction)

filename.mrc

0.623382

0.5817


In the above screenshot shown, a list of all filename.enr.mrc is displayed in the file list. For every filename.enr.mrc chosen, the program will look for filename.efar.mrc.mat in the matfiles directory specified. The defocus stored in the filename.efar.mat file corrected by the defocus offset specified. Depending on the kind of correction specified, Phase only or  Phase and  Amplitude correction is  applied to filename.enr.mrc. The corrected file is stored in the "correct" directory with the filename filename.enr.mrc.ctf_ph.

See also documentation for aceacedemoleginon_ace_gui and leginon_ace_correct .

© 2004-2005 Satya P. Mallick