Appion

h1. Create full tomogram

!http://emg.nysbc.org/attachments/273/Picture_71.png!

h2. General Workflow:

# Select the tiltseries for which a tomogram is to be calculated.

# Select the alignment run from [[Align tilt series]] to be used.

# Check the run name and enter a description.

# 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.

!http://emg.nysbc.org/attachments/274/Picture_74.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 "Create full tomogram" submenu in the appion sidebar.

# Now click on the "1 Complete" link under the "Create full tomogram" submenu. This opens a summary of all tomograms that have been calculated for this dataset.

!http://emg.nysbc.org/attachments/275/Picture_77.png!

# Clicking on the "id" opens a summary page for the calculated tomogram that includes input parameters and file directory paths.

# In order to [[Upload full tomogram|upload this tomogram]] for further processing, click on the "Upload full tomogram" link in the Tomography menu on the Appion Sidebar.

!http://emg.nysbc.org/attachments/276/Picture_80.png!

h2. Notes, Comments, and Suggestions:

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[[Align tilt series|< Align Tilt Series]] | [[Upload full tomogram|Upload Tomogram >]]

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