Appion

h1. Create tomogram subvolume

In order to upload subvolumes of a tomogram, the user first needs to use the [[particle selection]] tool to pick which portions of the full tomogram to upload.  The protocol for this step, as well as creation of the subvolume, is outlined below.

h2. General Workflow:

# In the Appion Sidebar, select the "manual picking" option under the "Particle Selection" submenu.

# Check the run name and output directory.

# Select the "zproj" present from the dropdown menu.  This means that you will be selecting portions of your tomogram using only these images.

# Set a diameter for the resulting images (won't affect actual boxing, just display).

# Check the commit to database box if desired.

# Click the "Just Show Command" button.

!http://emg.nysbc.org/attachments/330/Picture_68.png!

# A new window will open with a command that can be copied and then:

# pasted into a unix terminal to run.  NOTE:  Manual picker cannot be run from the webpage!

!http://emg.nysbc.org/attachments/331/Picture_71.png!

_# Many more steps to come......_

# To [[Average tomogram subvolumes|average multiple tomogram subvolumes]], click on the "Average tomogram subvolumes" link in the "Tomography" submenu on the Appion sidebar.

h2. Notes, Comments, and Suggestions:

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[[Create full tomogram|< Create Full Tomogram]] | [[Average tomogram subvolumes|Average Tomogram Subvolumes >]]

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