1. Simplify the display Show only alpha carbons
Turn off show backbone oxygen
Color secondary structure
Turn 3 D display on

2. 1HEW Backbone as ribbon Sidechains only in binding pocket
Substrate in yellow
Non-polar residues of binding pocket in turquoise

3. 1HEW Backbone as alpha carbons Sidechains only Tyr62
Substrate with VDW surface and CPK colors

4. 1bmf

5. 1bmf
Colored by chain
(discuss similarity to helicase and T3SS)

6. 1bmf Open pdb – check chain id
Select Chain E (by clicking in column designation in Control Panel)
Safe selected residues in current layer as betaTP
Repeat for betaDP, betaE, alpha TP, alphaDP, and alpha E.

7. The save menu

8. 1bmf Open the three beta SU
<SHIFT> Color in in secondary structure (shift makes it act on the 3 layers simultaneously)

9. 1bmf 3 beta subunits
Use Magic fit and interative magic fit to align the three subunits (use betDB as reference layer)
<ctrl>tab allows you to move through the three layers
For an animated GIF see

10. Layer Info Window
Checkmarks in the vis and mov columns provide a fast way to change settings for the different layers

11. betaTB and betaE with RMS coloring compared to betaDP
Magic fit -> fit molecules -> RMS coloring
RED: Long wavelength = long distance between structures
BLUE: Short wavelength = short distance between structures
If you need to switch the reference layer, you can do so in the SwissModel menu

12. The 3 point alignment tool
If you want to compare the structure of very dissimilar proteins that use a similar substrate, sometimes it helps to align the substrates.
This can be done through the 3 point alignment tool.