Align tilt series » History » Revision 21
Revision 20 (Anke Mulder, 06/07/2010 10:54 AM) → Revision 21/29 (Anke Mulder, 06/07/2010 11:00 AM)
h1. Align tilt series !http://emg.nysbc.org/attachments/267/Picture_62.png! h2. General Workflow: # Select the tiltseries to align. # Check the runname and enter a description. # Use the radio button to select Protomo Refinement or IMOD shift-only alignment. # To submit the job to the cluster click the "Align Tilt Series" button. Alternatively, click on "Just Show Command" to obtain a command that can be pasted into a UNIX shell. !http://emg.nysbc.org/attachments/263/Picture_55.png! # 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 "Aliogn tilt series" submenu in the appion sidebar. # Now click on the "1 Complete" link under the "Align tilt series" submenu. This opens a summary of all tilt series alignment runs that have been completed for this dataset. !http://emg.nysbc.org/attachments/266/Picture_61.png! # Clicking on the "alignrun id" opens a summary page for the alignment cycles that were run. # Clicking on the "refine cycle" number opens a report page for that cycle including input parameters and directory paths. Clicking on "Alignment Movie" opens a new web-browser with a movie of the aligned tilt series. # The same alignment cycle can be repeated by clicking "Repeat Last Aligner Iteration" or another initiated by clicking "Setup Next Aligner Iteration" (See Step 11 below). # In order to [[Create full tomogram|calculate a tomogram]] from the aligned tiltseries, click on the "Create full tomogram" link in the Tomography menu on the Appion Sidebar. !http://emg.nysbc.org/attachments/272/Picture_70.png! # If you selected "Repeat Last Aligner Iteration or "Setup Next Aligner Iteration" in step 9: Enter the tilt image that protomo should use as a starting point. Note that once you've entered this image number, the corresponding image is surrounded by a blue circle in the tilt-series graph. # Enter a description of this run. For example "repetition of alignrun id 5". # Click "Align Tilt Series" to submit to the cluster. Alternatively, click "Just Show Command," to copy and paste the command into a unix shell. 9, then: h2. Notes, Comments, and Suggestions: ______ [[Tomography|< Tomography]] | [[Create full tomogram|Create Full Tomogram >]] ______