Home > PyMOL > Cavity and Pocket

Cavity

  1. Preparation
    2. First, turn off all displays and display the surface and ribbon models. (*This operation is OK as long as the surface is displayed. You can turn off the cartoon model or display the ribbon model as you like.)

    From the command line or the object panel.
    hide everything
    show surface
    show ribbon


  2. Display cavity
    3. From External GUI
    Setting → surface → Cavities & Pockets(Culled)



  3. Adjustment
    4. Even small cavities are displayed, adjust the numbers to remove the small cavities.
    set cavity_cull, 34


  4. Change color
    5. Change the surface to your preferred color.
    set surface_color, marine


  5. Transparent
    6. To make a surface transparent, go to External GUI
    Settings → Transparency → surface → 40% (the number is up to you).



Pocket

Let's try displaying the molecular surface only around the ligand. The example uses PDB ID: 3A7E. The ligand is displayed as a ball-and-stick model.
  1. Select the area around the ligand
    2. Use the following command. This means "select 8 Å around sam with the name pocket." Replace sam with the name of the ligand and replace the number around 8 with the distance you want to display.
    select pocket, resn sam around 8

    If you don't know the name of the ligand, display the sequence with Display → Sequence and look for the three-letter name (SAM is used in this example).


  2. Show Surface
    3. From the panel (pocket) created in step 1, select
    Show → surface
    to display the molecular surface.


  3. Change the color
    4. Change the surface color with the following command.
    set surface_color, marine
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