Align tilt series¶

General Workflow:¶

1. Select the tiltseries to align.
2. Check the runname and enter a description.
3. Use the radio button to select Protomo Refinement or IMOD shift-only alignment.
4. 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.
   
5. 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.
6. 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.
   
7. Clicking on the "alignrun id" opens a summary page for the alignment cycles that were run.
8. 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.
9. 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).
10. In order to calculate a tomogram from the aligned tiltseries, click on the "Create full tomogram" link in the Tomography menu on the Appion Sidebar.
    
11. 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.
12. Enter a description of this run. For example "repetition of alignrun id 5".
13. Click "Align Tilt Series" to submit to the cluster. Alternatively, click "Just Show Command," to copy and paste the command into a unix shell.

Notes, Comments, and Suggestions:¶

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