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Chemistry LibreTexts

5.5: Interactive Molecule and Protein - Molecule Generator

  • Page ID
    158786
  • This is the seven-step workflow to embed an interactive protein figure like that below. It is similar for embedding a molecule, but uses the PDB database.

    The seven steps (from start to finish) for embedding interactive proteins/molecules via the molecular generates are:

    • Step 1 (Prepare the image)
    • Step 2 (Copy Code)
    • Step 3 (Navigation and Edit)
    • Step 4 (prepaste)
    • Step 5 (paste)
    • Step 6 (save and tag)
    • Step 7 (refresh)

    Step 1: Prepare the image

    Step 1 (Prepare the image): Go to

    https://bio.libretexts.org/Visualizations_and_Simulations/Molecular_and_Protein_Interactive_Figures/Molecule_Generator

    and organize how you want the image to go. Since you will probably want proteins most, select "www.rcsb.org PDB ID" under the option (see red arrow in image below).

    clipboard_e0624fd6b011e294fd232b585dcc9361d.png

    Then you put in the PDB code you want. For example "3PYP" for my favorite protein. That pops up the full menu of options including the way the interactive figure will look. Tweak with the options as you like (most are obvious).

    Step 2: Copy Code

    Step 2 (Copy image code): Press the blue button "Copy GLmol to Clipboard" (see red arrow in image below).

    clipboard_e0402e91af1a00ac6dee87b186f0f666b.png

    Steps 3 & 4: Navigate, Edit and Prepaste

    Step 3 (Navigation and Edit): Go to the LibreTexts page you want to embed that code and "edit" the page.

    Step 4 (prepasting): In the spot you want the image to go to "style" and click on "Dekiscript" to add a block to the code.

    clipboard_ea62f71a504b7e1a0e4d1007f9450348b.png

    It will look like this:

    clipboard_e18bcd494ea13e0bbe4a769116786fdf5.png

    Steps 5 and 6: Paste and Tag

    Step 5 (paste): Paste the code that was saved in step 2 from your clipboard to the red Dekiscript block under "Enter Dekiscript")

    Step 6 (save and tag): Save the page, and under page settings (it may be expanded or not) you will see a "Embed GLmol" option (see red arrow below)

    clipboard_edecb00903e64ce9c7ca25c128d2f925f.png

    The organization of the page settings is not standardized across the libraries; the one above is for chemistry and biology is organized differently, but find the proper tag and switch it to "yes"

    Step 7: Refresh

    Step 7 (refresh): Refresh the page (e.g., F5 on PCs) and be amazed at the embedded protein in your page.