Frealign Refinement¶

General Workflow:¶

1. Select the non-CTF corrected stack of particles to use for refinement from the dropdown menu.
2. Select the non-CTF corrected stack of particles to use for the final reconstruction from the dropdown menu.
3. 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 in the Appion Sidebar.
4. Click "Use this stack and model" to proceed to the next step.
   
5. Check the Run Name and Output Directory.
6. Use the radio button to choose initial orientation parameters. These can be imported from a previously run EMAN reconstruction, or determined by Frealign.
7. Set cluster parameters as is appropriate.
8. 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.
9. 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.
   
   h2. Notes, Comments, and Suggestions:

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