Align tilt series » History » Revision 17
Revision 16 (Anke Mulder, 06/03/2010 06:18 PM) → Revision 17/29 (Anke Mulder, 06/03/2010 06:19 PM)
h1. Align tilt series !http://emg.nysbc.org/attachments/267/Picture_62.png! h2. General Workflow: # Select the tiltseries for which a tomogram is to be calculated. # 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". # In order to [[Create full tomogram|calculate a tomogram]] from the thte 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! h2. Notes, Comments, and Suggestions: ______ [[Tomography|< Tomography]] | [[Create full tomogram|Create Full Tomogram >]] ______