"

II.B. iCn3D Changing Color and Representation (Alternative Renderings)

Henry V. Jakubowski and Kristen Procko

Overview: This chapter shows how to change the representation (rendering) of a protein in iCn3D.

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 iCn3D – https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html
  2. In the popup window, where it says: “List of PDB, MMDB, or AlphaFold UniProt structures“, type 1XWW. Click the button that says “load biological unit”.

Note: Default rendering is ribbon (cartoon) with black background and small molecules shown as sticks

Alternative Renderings

  1. From the dropdown menu: Style → Protein → then select each of the available choices
Screenshot of dropdown menu with 'proteins' and 'C Alpha Trace' highlighted for selecting protein rendering types.
Figure 1: Selecting the rendering type of the protein
  1. For your favorite protein renderings, explore coloring. In the dropdown menu: Color → then pick available choices.
    o Try Secondary, Sheets in Yellow
    o Charge
    o Hydrophobicity
    o Solvent accessibility
  2. Before the next step, use the dropdown menu to select: Secondary → Sheet in Yellow
Screenshot highlighting the option for selecting by secondary structure with ‘secondary structure’ highlighted in the first dropdown and ‘sheet in green’ highlighted in the second.
Figure 2: Selecting by secondary structure
  1. To view side chains: Style → Side Chains → Sticks (they will remain same color as secondary
    structure for now). The color of SO42- and bound glycerol will default to CPK
Screenshot of the tool to change side chain rendering with ‘side chains’ highlighted in the first menu and ‘stick’ highlighted in the second menu.
Figure 3: Changing side chain rendering
  1. In the dropdown menu: Style → Background → White

Save Files

  1. Save the file in two ways. Using the dropdown menu:
  • Save an iCn3D PNG image: a) File → Save Files → iCn3D PNG image → original size
    • In the popup window, type a name.
    • File can be reloaded in iCn3D: File → Load → iCn3D PNG IMAGE)
  • Save an iCn3D share link: File → Share Link → Save → Lifelong Short Url.
    • Copy and paste the link into a text file to save it.
Jump to the next iCn3D tutorial: III.B. iCn3D Surface Properties

License

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

Share This Book