Appion

h1. CtfFind Estimation

This algorithm works on tilted images.

!http://emg.nysbc.org/attachments/251/Picture_36.png!

h2. General Workflow:

# Make sure that appropriate run names and directory trees are specified.  Appion increments names automatically, but users are free to specify proprietary names and directories.

# Select the leginon preset corresponding to the images you'd like to process.  Generally "_en" images in leginon are the raw micrographs, but uploaded film data will have a different present.  Selecting "all" will simply process all images.

# Check boxes allow the option to run Ace 2 concurrently with data collection.  "Wait for more images" will wait until collection times out before stopping ACE 2 processing.  The "Limit" box allows restrictions on the number of images to process, which is useful when testing parameters initially. 

# Radio buttons under "Images to Process" allows a level of pre-processing image filtering.  Images that were rejected, hidden, or made exmplars in the image viewer can here be included or exluded.  

# Radio buttons under "Image Order" sets the order in which images are processed and radio buttons under "Continuation" gives the option of continuing or rerunning a previous ACE 2 run.

# If you have a previous ACE1 or Ace 2 run, check this box and set a confidence value to reprocess images that scored below that confidence value.  Otherwise, leave unchecked.

# Make sure that "Commit to Database" box is checked.  (For test runs in which you do not wish to store results in the database this box can be unchecked).

# Click on "Run Ace 2" to submit your job to the cluster.  Alternatively, click on "Just Show Command" to obtain a command that can be pasted into a UNIX shell.

!http://emg.nysbc.org/attachments/249/Picture_34.png!

# If your job has been submitted to the cluster, a page will appear with a link "Check status of job", which allows tracking of the job via its log-file.  This link is also accessible from the "1 running" option under the "Run Ace 2" submenu in the appion sidebar.

# Now click on the "1 Complete" link under the "Run Ace 2" submenu.  This opens a summary of all Ace 2 runs that have been done on this dataset, including a summary histogram of confidence values for all Ace 2 runs.

!http://emg.nysbc.org/attachments/250/Picture_35.png!

# Clicking on "download ctf data" opens a dialog for exporting Ace 2 results for use in another application.

# Clicking on the "acerun#" name opens a summary page of the parameters used for the particular run.

# The CTF parameters and astigmatism estimation determined by Ace 2 can be applied to particles during particle boxing in appion with the [[Stack_Creation|Create Particle Stack]] tool.

!http://emg.nysbc.org/attachments/247/Picture_22.png!

h2. Notes, Comments, and Suggestions:

# Ace 2 is faster than ACE 1

# If multiple ACE1 and Ace 2 runs are performed for a single dataset, the Appion stack creation tool will select the CTF parameters determined with the highest confidence value for a particle from a given micrograph.  

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[[CTF Estimation|< CTF Estimation]] | [[Stacks|Create Particle Stack >]]

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