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V.B. iCn3D Mouse/Trackpad Selection

Henry V. Jakubowski and Kristen Procko

Overview: This activity demonstrates how to select and label parts of a macromolecular structure

Outcome: The user will be able to identify parts of a macromolecule of interest, select them with the mouse/trackpad, and save them as separate objects.

Time to complete: 15 minutes

Modeling Skills

  • Selecting groups in the structure viewer window with the mouse
  • Saving selected groups
  • Rendering selections separately

About the Model

PDB ID: 6m0j

Protein: SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

Activity: Angiotensin-converting enzyme 2 (Chain A); Spike protein S1 (Chain E); NAG – glycan; Zn2+; Cl–

Description: Receptor for SARS-CoV-2 pandemic virus

Steps

Load Structure

  1. Open iCn3D – https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html
  2. In List of PDB, MMDB, or AlphaFold UniProt structures, type 6M0J
  3. Click “load biological unit”.

Note: Default render is ribbon (cartoon) with black background. Note the S-S bonds (yellow sticks) and Glycan (CPK colored sticks).

  1. To view glycans, we will first ensure iCn3D is in the full menu mode. In the upper left-hand corner, click the down arrow and select “all” to display all menu items.
Screenshot of NCBI website interface, highlighting the menu option to go from “simple” set to "All" for viewing glycans.
Figure 1: To view glycans, the menu should be set to “All”
  1. In the dropdown menu: Style → Glycans → Show Cartoon to display an overlay of the  SymbolicNomenclature for Glycans (SNFG)

Selecting Residues or Ions with the Mouse

  1. In the dropdown menus: Select → Select on 3D → Residue (ensure residue is selected by clicking on it)
Screenshot of the “select” menu with “select on 3D” and “residue” highlighted, which enables the selection of individual residues.
Figure 2: Setting up iCn3D to select with the mouse
  1. Rotate and zoom the structure so that the dark sphere is visible and unobscured. It is best if there are no parts of the protein behind it. With the mouse or trackpad, hover over Zn
  2. Alt+Click (Option+click on Mac) and a yellow halo will appear around it (ions are considered residues for selection)
Unobscured brown sphere (Zn2+) highlighted with a yellow halo with magenta and blue protein cartoon structure surrounding it.
Figure 3: View following Step 8
  1. Save the Zn ion selection:

a) Using the dropdown menu: Select → Save Selection

b) In the popup window that comes up, name it Zn

Computer screen displaying "Save the Selection" in a popup for selecting zinc.
Figure 4: Setting zinc in the save selection popup

c) Click “save”

  1. Select and save a selection for the Cl ion

a) Alt+Click (Option+click on Mac) on the Cl ion

b) Use the dropdown menu to save: Select → Save Selection

c) In the popup window that comes up, name it Cl

d) Click “save”

Note: To save both ions as one selection, you can select multiple objects. First, Alt-click Zn and then Ctrl+click Cl to add it to the current selection.

Selecting Chains with the Mouse

  1. Using the dropdown menus, change the selection mode to select chains: Select → Select on 3D → Chain (click on the word chain)
  2. Alt+Click blue chain (Sars-Cov2-Spike S1 Receptor BD)
  3. Save the selection

a) Using the dropdown menu: Select → Save Selection

b) In the popup window that comes up, type SpikeRBD

  1. Alt+Click pink chain (ACE-2)
  2. Save the selection

a) Using the dropdown menu: Select → Save Selection

b) In the popup window that comes up, type ACE2

Note: You may need to click the blue chain again to deselect it after clicking on ACE2. It appears that chain selection behaviors may not be the same as residues.

Rendering

  1. In Selected Sets popup that appears to the right, click ACE2 if it is not already selected
Screenshot of the Select sets tool showing the menu of Defined Sets with ACE2 highlighted.
Figure 5: Selections appear in the Select Sets popup menu
  1. Using the dropdown menus: Color → Unicolor → Gray → Light Gray
Screenshot of the color analysis tool, showing the color menu for selecting colors with “gray” and “light gray” highlighted.
Figure 6: Using the color menu to set the color of a selection
  1. In Selected Sets popup that appears to the right, click Spike-RBD
  2. Using the dropdown menus: Color → Secondary → Sheets in Yellow
  3. Change the background to white using the dropdown menu: Style → Background → White
  4. To clear the yellow highlight, there are two options:

a) In the dropdown menu: Select → Clear Selection

b) In the dropdown menu: Select → Toggle Highlight

  1. (Optional) Save the file using the dropdown menu: File → Share Link → Save short URL
    See example
Final output of the tutorial: a protein model displayed in grey, blue, an yellow with ions as green and red spheres.
Figure 7: Final output of this tutorial

Jump to the next iCn3D tutorial: VI.B. iCn3D Selection Tools

License

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

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