Appion

h1. Ace Estimation

!http://emg.nysbc.org/attachments/243/Picture_17.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.

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

# Check boxes allow the option to run ACE concurrently with data collection.  "Wait for more images" will wait until collection times out before stopping ACE 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.  Radio buttons under "Continuation" gives the option of continuing or rerunning a previous ACE run.

# Select the sample preparation method.  Default parameters differ for ice and negative stain.

# 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" 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/244/Picture_18.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" submenu in the appion sidebar.

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

!http://emg.nysbc.org/attachments/242/Picture_16.png!

# 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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