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VI.C. Mol* Selecting on the Sequence and Labeling

Didem Vardar-Ulu and Shane Austin

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

Load the Structure:

  1. Go to rcsb.org
  2. In the search bar at the top, type: 1xww and press Enter.
  3. On the landing page, click the “Structure” tab next to the highlighted “Structure Summary” tab to open the user interface and load the structure.
  4. Hide the “Ligand”, “Water”, and “Ion” components listed in the “Structure Panel” by clicking on the “eye” icon next to them.

Select part of the molecule by sequence: (Figure 1)

Computer screen displaying instructions for coloring chains, highlighting the 1) selection model toggle and 2) picking level.
Figure 1: Changing selection mode for sequence. See text for arrow descriptions.
  1. Activate the “Select Mode Toggle” by clicking the “cursor” icon (Arrow 1).
  2. Choose your picking level as “Residue” (Arrow 2).
  3. Click on the first residue you want to select in the Sequence panel (e.g., C12) and drag to the last residue you want to select (e.g., R18, Arrow 3). This will highlight the selected region in green on the sequence and the 3D canvas.

 

Note: Hovering your cursor on any part of the sequence or structure will display information about the PDB ID, model number, instance, chain ID, residue number, and chain name listed at your chosen picking level at the bottom right corner of the 3D canvas.

  1. Create a new component (e.g., P-loop) as described in Chapter V.C “Create a new component from selected elements”. During component creation, choose “Ball and Stick” for the “Representation” to show this selection’s sidechains and label your component “P-loop”.

Show Label on the Structure: (Figure 2)

You can label a component as a whole or select individual parts (e.g., residue) to apply separate labels.

Screenshot of the measurements tool highlighting steps 1-5 for labeling the p-loop.
Figure 2: Showing labels on the structure
  1. Label the P-loop:
        1. Click on the three dots next to the component “P-loop” (Arrow 1)
        2. Click “select this” (Arrow 2)
        3. Click “Measurements” (Arrow 3) to open up a drop-down menu.
        4. Click “Add” (Arrow 4) and click “Label” (Arrow 5). Use the instructions in the next section “Customize Labels”, to modify the label.
      1. Label residues in the P-loop:
        1. Click on the residue you want to label on the sequence or 3D canvas.
        2. Click “Measurements” (Arrow 3) to open up a drop-down menu.
        3. Click “Add” (Arrow 4) and click “Label” (Arrow 5). Use the instructions in the next section “Customize Labels”, to modify the label.

 

 

 

Note: Labels are created near the center of the component or selection in the default format, which you can further modify.

Customize Labels: (Figure 3)

Screenshot of the measurements tool highlighting steps 1-5 for customized labeling.
Figure 3: Customizing labels on the structure
      1. Click “Labels” to see a list of all the created labels (Arrow 1)
        Image of a cartoon representation of a protein with “P-loop” labeled.
        Figure 4: Labelled P-loop on 1xww
      2. Click the three dots next to the label you want to modify. (Arrow 2)
      3. Click “Options” to activate a drop-down menu. (Arrow 3)
      4. Enter the name for your label in the cell next to “Text” (Arrow 4)

 

 

 

 

Note: In this same drop-down, you can change the text size, color, opacity, and quality of the label. When you click “Advanced Options” (Figure 3, Arrow 5), you can gain access to numerous additional controls, including location (offset x, offset y, offset z).

 

Jump to the next Mol* tutorial: VII.C. Mol* 5A Selection

License

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

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