Appion

h1. Ace Estimation

_"ACE: automated CTF estimation." (2005) Mallick SP, Carragher B, Potter CS, Kriegman DJ. Ultramicroscopy. v104(1).  PMID: 15935913_.

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.

# If tilted data was collected, a dropdown menu provides the option to run CTF correction on selected subsets of tilted or untilted images.

# 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 Maxlike Alignment" 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.

# 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 Alignment" submenu in the appion sidebar.

# Once the job is finished, an additional link entitled "1 ready to upload" will appear under the "Run Alignment" tab in the appion sidebar.  Click on this link, and a page will open with a summary of the run output.  Clicking on the link next to "reference stack" will open a new window that shows the class averages obtained via this analysis.

# If you are satisfied with the alignment and want to continue processing its output, click on "Upload Job".  This shouldn't take too long to finish.

# Now click on the "1 Complete" link under the "Run Alignment" tab.  This opens a summary of all alignments that have been done on this project.    

# Click on the link next to "reference stack" to open a window that shows the class averages and that contains tools for exploring the result.  Such tools include the ability to browse through particles in a given class, create templates for reference based alignment, substack creation,3D reconstruction, etc.

# To perform a feature analysis, click on the grey link entitled "Run Feature Analysis on Align Stack ID xxx".

!http://emg.nysbc.org/attachments/210/Picture_115.png!

h2. Notes, Comments, and Suggestions:

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

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