LEGINON ACE DOCUMENTATION


 

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

  2. Run Name : You can process the same experiment multiple times. Run names lets you differentiate between them. 
  3. Database Type: The two database types are Leginon1 and Leginon2 . In Leginon1 the Kilovolts (KV) and pixel size (ps) cannot be queried and so the user has to provide that information.  Leginon 1 option is not tested extensively. In future versions Leginon 1 will not be supported. The "Configure Database" button allows you to specify your databases. 

  4. Boolean: 

  5. File Type:  Choose the file type and the corresponding file filter. The file types foc, efar and enr correspond to focus, far from focus and near to focus  respectively.

  6. Directories : 

  7. Advanced: 

  8. File List box:  Shows the list of file of the type selected. A single file can be selected by clicking on the filename. Multiple files can be selected by CTRL+click or (click and drag) and all files can be selected by CTRL+A.

  9. Viewer: The viewer you would like to see your images. If gqview is used, it takes you to the correct output directory. Other viewers (like xv ) are simply launched.

  10. View Output: Launches the viewer.

  11. Process:  Starts processing of the selected images.

  12. Help:  Displays this page.

  13. Error Report:  ACE logs everything  that is typed or output in the command prompt in a file named "session.log". A screenshot is also generated when you press the "Process" button. In the case of a crash, you can restart leginon_ace_gui and click on the error report. The file "session.log" and "screenshot.png" will be displayed so that the user knows exactly what would be sent as error report. You may choose to edit session.log to report only the last run.
  14. Zip Report: Zips the files "session.log" and "screenshot.png" into "report.zip" which you can email me.
  15. Console Output: The console (the command prompt in MATLAB desktop ) displays partial results in the following format. An example is also shown.  

     

         Filename 

     Nominal Defocus

     Crude defocus estimate 

    Refined defocus1  estimate 

    Refined defocus2 estimate

    Amplitude contrast 

    Astigmatism ratio

    Astigmatism angle 

    Confidence on results

    filename.mrc

     2.000000 

    2.068837

     1.975

     2.15

     0.06

     0.96

     55.5

    0.95

See also documentation for ace, acedemoacedemo_correct  and leginon_ace_correct .
© 2004-2005 Satya P. Mallick