Frealign Refinement » History » Revision 11
Revision 10 (Anke Mulder, 06/07/2010 01:33 PM) → Revision 11/24 (Anke Mulder, 06/07/2010 01:38 PM)
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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