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.  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 "Frealign Refinement" submenu in the appion sidebar. 

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

# Once the job is finished, an additional link entitled "1 prepared" will appear under the "Frealign Refinement" tab in the appion sidebar.  Click on this link.

# Use the radio button to choose the prepared frealign job you want to launch.

# Click "Use this prepared job" to proceed to the next step. 

!http://emg.nysbc.org/attachments/307/Picture_30.png!

# Select the cluster to which you would like to submit this job.

# Check wall and CPU time parameters.

# Click "Show Job File".  This opens another window containing directions for final submission of the refinement.  Below the directions, a copy of the job file is displayed.

# Click "Put files in DMF".  This opens a pop-up window containing DMF commands.

!http://emg.nysbc.org/attachments/308/Picture_36.png!

# Copy the dmf commands.

# Open a terminal, and paste the dmf commands.

!http://emg.nysbc.org/attachments/309/Picture_37.png!

h2. Notes, Comments, and Suggestions:

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

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