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General Information

Here are general information about the Protein PyMOL Scene Configuration.

Protein PyMOL Scene Configuration

  • Overview

    With the Protein PyMOL Scene Configuration you can ...

    • change the color of the selected protein chain.
    • color atoms by element color.
    • change the background color.
    • show or hide hydrogen atoms.
    • display the selected protein chain as cartoon.
    • display the selected protein chain as sticks.
    • display the selected protein chain as ribbon.
    • display the selected protein chain as lines.
    • display the selected protein chain as spheres.
    • display the selected protein chain as dots.
    • display the selected protein chain as mesh.
    • display the selected protein chain as surface.
    • hide all representations.

Getting Started

Change the color of a protein chain

  1. Select a protein from the tree.
  2. Click on , to load the pymol session of the selected protein.
  3. Select a chain from the tree.
  4. Click on one of the colors in the color grid.

Color the atoms of a protein chain by their element

  1. Select a protein from the tree.
  2. Click on , to load the pymol session of the selected protein.
  3. Select a chain from the tree.
  4. Choose a representation other than Cartoon or Ribbon.
  5. Click on Color besides Atoms by Element. (Click on Reset to return to the previous color.)

Change the background color of the current session

  1. Select a protein from the tree.
  2. Click on , to load the pymol session of the selected protein.
  3. Select a chain from the tree.
  4. Toggle the White Background button to On.

Show or hide all hydrogen atoms of a protein chain

  1. Select a protein from the tree.
  2. Click on , to load the pymol session of the selected protein.
  3. Select a chain from the tree.
  4. Click on Show to display the hydrogen atoms. (Click on Hide to hide the hydrogen atoms again.)

Details

  • Cartoon and Ribbon representation cannot be used to color Atoms by Element.
  • Every PyMOL session has a black background by default. The background can be changed to white using the toggle.
  • Show always adds hydrogen atoms to the current active representations. This means that some representations may show hydrogen atoms while others may not.

See Also

Load Protein PyMOL Session Add Protein PyMOL Scene Update Protein PyMOL Scene Delete Protein PyMOL Scene

Proteins