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VI.A. ChimeraX Selecting on the Sequence and Labeling

Walter Novak and Josh Beckham

Overview: This activity demonstrates how to select parts of a macromolecular structure using the sequence display.

Outcome: The user will be able to select parts of a macromolecule using the sequence, and purposefully modify their display.

Time to complete: 15 minutes

Modeling Skills

  • Using the sequence to create selections
  • Labeling parts of the molecule

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

Note: From the literature, it is known that the active site contains a nucleophilic cysteine residue at position 12 in the sequence. It is part of the phosphate-binding loop (P-loop) made up of amino acid residues 12-18 (sequence: CLGNICR). Let’s find, select, and render these amino acids.

Load and Prepare the Structure

  1. Load 1xww. In the command line, type: open 1xww
  2. Hide all of the displayed residues. Ensure you are in the “Home” toolbar selector and under the “Atoms” toolbar click ”Hide.”

Selecting by Sequence

  1. Turn on the Sequence Viewer. In the pulldown menu, click “Tools” → Sequence → Show Sequence Viewer (Figure 1).
Image of software interface displaying the tools menu, highlighting 'sequence' and 'show sequence viewer' options.
Figure 1: Opening the sequence viewer
  1. In the popup window, click “Show” (Figure 2).
Popup window displaying the show chain sequence feature with group identical sequences checked.
Figure 2: The “Show Chain Sequence” popup window
  1. Click on C12 in the sequence (Note: Hovering over the amino acid in the sequence gives the number), and drag to R18. Notice the residues become highlighted in the sequence and on the structure in the structure viewer window (Figure 3).
Computer screen displaying a program with a protein image and a yellow arrow pointing to the protein's amino acid sequence.
Figure 3: The Sequence Viewer
  1. Define this current selection as “PLoop.” In the dropdown menu: Select → Define Selector. In the popup window that comes up, type Ploop and click “OK”.
Screenshot of the define selector box with ‘current selection’ highlighted and named ‘Ploop’ in the text entry box.
Figure 4: Labeling the P-loop
  1. Display the side chains in the P-loop as sticks by clicking “Show” in the “Atoms” area of the “Home” toolbar (Figure 5).
  2. Make the selection the center of focus.  Using the dropdown menu: Actions → Focus.
    3D rendering of the output from step 7 displaying the p-loop.
    Figure 5: Output from Step 7

Labeling Residues and Rendering

  1. Label the residues using the dropdown menu: Actions → Label → Residues → Name and Number.
Screenshot showing the actions menu with options to label residues with name and number highlighted.
Figure 6: Using the actions menu to label residues
  1. Resize the labels to 1.2 Ångstroms.

In the command line, type: label height 1.2

  1. You may also change the label color in the ”Color Actions” popup window.

a) Dropdown menu: Actions → Color → All Options

b) Ensure “Labels” is checked for “Coloring applies to:”

c) Select the checkbox “Show all colors.”

d) Select “Plum” from the list. (Output shown in Figure 7.)

Note: Alternatively, type in the command line: label color plum

Computer screen displaying a model of a protein with resized label residues for Cys 12, Leu 13, Gly 14, Asn 15, Ile 16, Cys 17, and Arg 18.
Figure 7: View of the resized and recolored label residues
  1. Display the sulfate as sticks.

a) In the dropdown menu: Select → Residues → SO4.

b) Click “Show” in the Atoms toolbar.

  1. Give the sulfate a custom label.

a) With the SO4 still selected, use the dropdown menu: Actions → Label → Residues → Custom Text.

b) Type: Sulfate in the box and click “OK.”

c) Make this label size 1.2 and plum-colored. Directions to do this using the command line:

label height 1.2

label color plum

Final output for steps in this chapter showing a 3D rendering of a protein structure, showcasing its complex arrangement and molecular details, including several labeled amino acid residues.
Figure 8: Final output

Finishing Up

  1. Change the background to white in the “Home” toolbar.
  2. (Optional) Save and close the session.

Jump to the next ChimeraX tutorial: VII.A. ChimeraX 5Å Selection.

License

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

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