Appion

h1. Frealign Refinement

!http://emg.nysbc.org/attachments/260/Picture_36.png!

h2. General Workflow:

# Select the non-CTF corrected stack of particles to use for refinement from the dropdown menu.

# Select the non-CTF corrected stack of particles to use for the final reconstruction from the dropdown menu.

# Use the radio button to select the initial model to use for refinement.  To upload an initial model click on the "Upload a new initial model" link or use one of the [[Import_tools|Import Tools]] in the Appion Sidebar.

# Click "Use this stack and model" to proceed to the next step.

!http://emg.nysbc.org/attachments/305/Picture_23.png!

# Check the Run Name and Output Directory.

# Use the radio button to choose initial orientation parameters.  These can be imported from a previously run EMAN reconstruction, or determined by Frealign.

# Set cluster parameters as is appropriate.

# Set specific Frealign parameters.  Use the mouse to point to an individual parameter, and a help-box will float above that option giving the required information for the user to choose the parameters.

# Click "Prepare Frealign" to submit to the cluster.  Alternatively, click "Just Show Command" in order to get a command that can be pasted into a unix shell.

!http://emg.nysbc.org/attachments/306/Picture_26.png!

h2. Notes, Comments, and Suggestions:

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[[Refine Reconstruction|< Refine Reconstruction]]|[[Quality_Assessment|Quality Assessment >]] 

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