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II.D. PyMOL Changing Color and Representation (Alternative Renderings)

Roderico Acevedo and Kristen Procko

Overview: This chapter shows how to change the representation (rendering) of a protein in PyMOL.

Outcome: The user will be able to select a particular rendering for a purposeful display of a protein.

Time to complete: 5–10 minutes

Modeling Skills

  • Loading structure
  • Alternative renderings
  • Saving files

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 Structure

  1. Open PyMOL by double-clicking on the application.
  2. In the top command line, type: fetch 1XWW, type=pdb1

 

Note: Default render is ribbon (cartoon) with black background, and small molecules shown as sticks or spheres (sulfate is shown as spheres, glycerol as sticks).

Alternative Renderings

Settings menu in rendering panel with the "S" button for displaying structure options indicated by the green arrow on the left and “C” for color indicated by the red arrow on the right.
Figure 1: Shows the names/object panel
  1. In the names/object panel, next to 1xww click the “S” (Show) button (Figure 1, green arrow) to display the structure in different ways. Each new representation is layered on top of the others.

Try:

S → lines

S → wire

S → ribbon

  1. Click the “H” (Hide) → ribbon to hide the ribbon presentation. This can be repeated for every representation.
  2. Now, try clicking “Show As” in the “S” button menu. This clears prior representations and only applies only the new representation to the structure.

Try: S → as → cartoon

  1. For your favorite representations, click the “C” (Color) button (Figure 1, orange arrow). Try the “by element” and “by ss” (secondary structure) coloring schemes.
  2. Click: C → by ss → the option where helix is red
  3. To display side chains, click: S → side chains → sticks
  4. To Ensure the main chain is hidden, click: H → main chain
  5. Apply the coloring in Step 6 and note the difference in sidechain display. 
Two types of molecules displayed: A) colored by secondary structure (magenta loops, red beta strands, and turquoise alpha helices), B) colored by element with carbon in gray.
Figure 2: Results of coloring. A) colored by secondary structure and B) colored by element, where carbon is gray.

Saving Files

There are two main file types for PyMOL. One is the “session file” that you can reopen and work on in PyMOL. The others are image files; PNG is a 2D file, and the other choices are 3D exports.

  1. Use the dropdown “Display” menu and select: Background → White
  2. In the file menu, click “Save Session”, select the location and type a file name.

    Note: Images can be made using the file menu, as well. In the file menu, click: Export image as → PNG

     

  3. In the Building buttons panel, click the “Draw/Ray” tab (see image above for camera icon).
  4. In the pop-up window, click “Draw” (faster rendering) or Ray (higher quality, but slower rendering).
  5. Click: “Save Image to File” to save as a PNG file.

 

Click here to go to Chapter III: Surfaces

License

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

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