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".
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.
    

Notes, Comments, and Suggestions:¶

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