Electron Density Map Fitting

Electron Density Map Fitting for Problem Set #7

Electron Density Map Fitting for Problem Set #7
		Rotate: Y 90° Y -90° Choose the Best-Fit R-Group: Residue 2 A B C D Residue 3 A B C D Residue 4 A B C D Background Color: White Blue Black
	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. (Please note: All 12 of the amino acid possibilities are falsely labeled, "ALA", however, a click on individual atoms will correctly identifiy that atom on the window status line. For example, if you click on the b-carbon of residue 56; the status line will read: `Atom:CB 424 Group ALA 56`.) Submit your proposed best-fit sequence along with an explaination of your approach. Feel free to submit an image of the fitted electron density with your problem set. [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.]

Rotate:

Y 90°

Y -90°

Choose the Best-Fit R-Group:

Residue 2 A B C D

Residue 3 A B C D

Residue 4 A B C D

Background Color:
White Blue Black

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.
(Please note: All 12 of the amino acid possibilities are falsely labeled, "ALA", however, a click on individual atoms will correctly identifiy that atom on the window status line. For example, if you click on the b-carbon of residue 56; the status line will read: Atom:CB 424 Group ALA 56.)
Submit your proposed best-fit sequence along with an explaination of your approach. Feel free to submit an image of the fitted electron density with your problem set.

[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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Original Page Design by Will McClure Last Modified March 18, 2003