To see the Ramachandran plot for all amino acids in this protein, click this button, or type "rama" in the console. The console can be brought up by right-clicking the JSmol icon, and selecting "console" from the pop-up menu.
The beta strands are colored gold, the alpha-helices are colored magenta. A short, connecting 310 helix is colored purple. The same color scheme is applied in the Ramachandran plot. Notice the scatter of the points outside of the typical alpha-helix and beta-sheet regions.
Open the console, by right-clicking on the Jmol window, and selecting Console near the bottom of the popup menu.
Now type display Gly to get the values of phi,psi angles for the Gly residues. Or any other amino acid (Pro, etc)
Type display all to show for all amino acids. Type model 1.1 to get the original structure back. (with water now showing)
Reset the protein
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