Overview: This chapter describes the application of coloring to help display molecular properties.

Outcome: The user will be able to display the molecular surface of a structure, apply a chemical property-based coloring scheme, and change transparency.

Time to complete: 10 minutes

Steps

Load the Structure

1. In the command line type: open 1XWW

Generate Molecular Surfaces and Surface Transparency

2. In the pulldown menu, click “Actions” → Surface → Show.
3. You may change the color of the surface independently. In the “Color Actions” panel (Actions → Color → All Options), ensure only “Surfaces” is checked in the “Coloring applies to:” section. Click on a color of your choice (Figure 1).

4. 

   To make the surface semitransparent, in the command line type: transparency #1 50, where “#1” is the model ID and “50” is 50% transparent. Alternatively, using the pulldown menu: Actions → Surface → Transparency → 50%. See Figure 2 for an example output.

Generate an Electrostatic Potential Surface

5. In the “Molecule Display” toolbar, click the “electrostatic” button.
6. ChimeraX will calculate the Coulombic potential and color the surface according to the calculated charge. Red = negative, white = neutral, blue = positive.
7. As above, this surface may be made semitransparent (Figure 3). (Tip: use the up arrow on your keyboard while in the command line to recall prior commands.)

Generate a Hydrophobicity Surface

8. In the “Molecular Display” toolbar, click the “hydrophobic” button.
   

   

9. ChimeraX will calculate the lipophilicity and color the surface. Dark goldenrod = more lipophilic (more hydrophobic), teal = less lipophilic (more hydrophilic).
10. As above, this surface may be made semitransparent (Figure 4).
11. (Optional) Save and close the session.

Jump to the next ChimeraX tutorial: IV.A. ChimeraX Viewing Biological vs. Asymmetric Units.