Frealign Refinement » History » Revision 15
Revision 14 (Anke Mulder, 06/07/2010 02:09 PM) → Revision 15/24 (Anke Mulder, 06/07/2010 02:10 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. 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. # Now click on "Submit job to Cluster." You can setup your Appion account such that you get email updates for refinements. !http://emg.nysbc.org/attachments/310/Picture_40.png! !http://emg.nysbc.org/attachments/309/Picture_37.png! h2. Notes, Comments, and Suggestions: ______ [[Refine Reconstruction|< Refine Reconstruction]]|[[Quality_Assessment|Quality Assessment >]] ______