Create full tomogram¶

General Workflow:¶

1. Select the tiltseries for which a tomogram is to be calculated.
2. Select the alignment run from Align tilt series to be used.
3. Check the run name and enter a description.
4. To submit the job to the cluster click the "Create Full Tomogram" 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 "Create full tomogram" submenu in the appion sidebar.
6. Now click on the "1 Complete" link under the "Create full tomogram" 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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