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3. Repeat step 1 for your volume with inverted contrast (basename_2Dbin2_inverted.rec). You should see a second green button appear in the Pool frame.
(D) Loading a NCMIR Logo
1. In the Pool frame, click the green 'Open Data' button. In the 'Look in' prompt, type the following: /home/aperez/amira/NCMIR_logo_IV
2. You will have three options. Each of the three options are different sizes, but all three will load in the lower left corner of the Viewer frame.
3. Choose which size you prefer, then click 'Load'.
4. Right-click on the new green button for the logo, and select IvDisplay. This will cause the logo to appear. If you do not like the size and would like to try another size, simply left-click on the green button for the logo and press the delete button, then load a new one.
(E) Display the Original Reconstruction
1. First, set the background color to solid black. In the upper menu, select View --> Background. Select the 'uniform' mode, then click on the color 1 button and select black. Click 'OK'.
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4. Move the Slice Number slider back and forth to scroll through the Z-slices of your volume. Notice how the slices appear to get smaller and bigger as you go up and down? This is because the camera is set to Perspective mode by default. To make the slice dimensions remain constant as you scroll through Z-slices, you need to change the camera mode to Orthographic. In the menu of icons above the Viewer frame, find the icon that looks like an eye with rays emanating from it. Click it once to switch to Orthographic mode:
| Center |
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5. Left-click on the OrthoSlice button. Click on the 'Edit' button under Colormap, and select 'Adjust to Histogram'. This will auto-contrast the tomogram.
6. If you are not satisfied with the auto-contrast, you can tweak it by clicking and dragging on the two indicators in the Colormap.
Pool --> Open Data --> Select Data --> MRC Volume
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