|Electron Density Map Fitting for Problem Set #7|
Five Amino Acid Residues in an Electron Density Map.|
The Chime image shows a short polypeptide, of sequence Gly-X-X-X-Gly, within its electron density map. The segment of a protein structure is initially shown as an Ala pentapeptide displayed as Backbone with beta carbons (if appropriate) and colored CPK. The meshwork surrounding the chain simulates the electron density contour from an X-Ray diffraction experiment (High resolution, <2.0 Å; see examples in the Lecture 22 notes).
Use the buttons (Labeled A-D) at the right of the model to find the best-fit amino
acid residue at each of the three positions (residues 2, 3, and 4). The buttons leave each amino acid
selected so that any combination of Display or Color can be used until another
amino acid is selected.
[Hints: The Ball & Stick (or Sticks) display is best for identifying the amino acid. Spacefill (or Dot Surface) should be used to assess how well each choice fits the contours. After you find a good fit at a position, rotate the model through 360° to be sure there is no missing (or excess) electron density when viewed from another perspective.]
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