Appion

h1. Spider Coran Classification

This method uses the Spider CA S command to run correspondence analysis (coran), a form of principal components analysis, and classify your aligned particles.  Spider commands are as described in _Frank, J. et al.  Journal of Structural Biology v116,190-199 (1996)_. 

h2. General Workflow:

_Note:  If you accessed "Run Feature Analysis" directly from an alignment run,  you will be greeted by the screen displayed on the left below.  Alternatively, if you accessed the "Run Feature Analysis Run" from the Appion sidebar menu, you will be greeted by the screen displayed on the right below._

# 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.

# Enter a description of your run into the description box.

# 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).

# Check that the appropriate stack of aligned particles are being analyzed, or choose the appropriate stack from the drop-down menu.  Note that stacks can be identified in this menu by alignment run name, alignment run ID, and that the number of particles, pixel and box sizes are listed for each.

# Click on "Run Spider Coran Classify" 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/181/Picture_52.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 Feature Analysis" submenu in the appion sidebar.

# Once the job is finished, an additional link entitled "1 complete" will appear under the "Run Feature Analysis" tab in the appion sidebar.  Clicking on this link opens a summary of all feature analyses that have been done on this project.    

!http://emg.nysbc.org/attachments/182/Picture_53.png!

# Click on the "alignstack.hed" link to browse through aligned particles.  

# To perform a feature analysis, click on the grey link entitled "Run Feature Analysis on Align Stack Id xxx" within the box that summarizes this alignment run.

!http://emg.nysbc.org/attachments/166/Picture_22.png!

h2. Notes, Comments, and Suggestions:

# WARNING: this method is very quick (~few minutes), but also very sloppy and does not always do a great job. The only way to obtain decent results is to run several times and compare the results.

# Particle-specific Radii parameters:  The default values are pretty good, but adjust as you see fit.  Make sure that your particle radius is appropriate!

# Alignment-specific Radii parameters:  These parameters allow you to specify the radius over which alignment will be done.  Generally a small first ring radius is used, and a last ring radius that just encompasses the particle is used; however, special samples might require a larger initial ring.

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[[Run_Alignment|<Run Alignment]] | [[Run Feature Analysis|Run Feature Analysis >]]

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