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III.D. PyMOL Molecular Surface/Properties

Roderico Acevedo and Kristen Procko

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

Modeling Skills

  • Display the Molecular Surface of Protein
    • Molecular with different colors
    • Electrostatic potential
    • Hydrophobicity

About the Model

PDB ID: 1XWW

Protein: Low molecular weight protein tyrosine phosphatase

Activity:  Hydrolyzes Tyr-OPO32-  phosphoester bond

Description:  Single chain, bound SO42- competitive inhibitor, bound glycerol (nonspecific stabilizer)

Steps

Load the Structure

  1. In the command line, type:  fetch 1XWW, type=pdb1

Generate Molecular Surfaces and Surface Transparency

  1. In the names/object panel, beside 1xww, click: S > Surface
  2. You may change the color of the surface, in the names/object panel, beside 1xww, click C and choose a color from the dropdown menu

Note: Changing colors using the names/object panel will change the color of all the atoms. For example, choosing green in the dropdown will change all atoms green and when surface is hidden, the underlying cartoon will also be green.

  1. To change the surface color independently, we use the command line. In the command line type: set surface_color, (color), 1xww
    where (color) is the color of your choosing. You can use the dropdown menu in C to view a list of color names.

    Color menu showcasing available choices including reds, greens, blues, yellows, magentas, cyans, oranges, tints, and grays.
    Figure 1: Color choices available in the color menu.
  2. To make the surface semitransparent, in the command line type: set transparency, 0.5
     where 0.5 is 50% transparent.

    Protein ribbon structure shown in blue surrounded by a blue semi-transparent molecular surface.
    Figure 2: Results of making surface semi-transparent.

Generate an Electrostatic Potential Surface

  1. In the dropdown menus, click Plugin → APBS electrostatics.
  2. In the pop-up box, click “Run”. A black pop-up will open and begin running calculations (this may require you to run PyMOL as administrator). A successful run will end with a small pop-up that says: “Finished with Success”.
Advanced configuration screen showing the APBS Electrostatics pop-up showing the "Run" button at the bottom right and the screen "Finished with Success" pop-up in the center.
Figure 3: The APBS Electrostatics pop-up window
  1. APBS will calculate the coulombic potential and color the surface according to the calculated charge. Red = negative, white = neutral, blue = positive.
Protein molecular surface with red (negative), blue (positive), and white (neutral) colors, illustrating APBS Electrostatics color mapping results with color bar on the bottom ranging from deep red (-5.000) to deep blue (5.000).
Figure 4: Results of APBS Electrostatics color mapping
  1. As above, this surface may be made semitransparent. To undo this, in the command line type: set transparency, 0

Note: The generated surface is overlayed onto any previously made surfaces. Make sure to hide any other surface renderings that may be turned on.

Generate a Hydrophobicity Surface

Note: PyMOL does not have an in-house plugin that will calculate hydrophobicity and plot its values onto a surface. There are scripts, such as color_h.py that will color protein molecules according to the Eisenberg hydrophobicity scale.

Click here to go to Chapter IV: Loading Structures

License

Seeing the Invisible: Learning to Teach with Biomolecular Visualization Copyright © by The BioMolViz Working Group. All Rights Reserved.

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