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Chemistry LibreTexts

1: INBRE workshop

  • Page ID
    192025
  • 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://chem.libretexts.org/Ancillary_Materials/Interactive_Applications/Molecular_and_Protein_Interactive_Figures/Molecule_Generator    (Chemistry)

    https://bio.libretexts.org/Visualizations_and_Simulations/Molecular_and_Protein_Interactive_Figures/Molecule_Generator    (Biology)

    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 Paste

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

    Step 4 (Paste the code): Go to the spot you want the image, then go to "Style", click on "Dekiscript" to add a block for the code

    clipboard_ea62f71a504b7e1a0e4d1007f9450348b.png

    This will give a block as below. 

    clipboard_e18bcd494ea13e0bbe4a769116786fdf5.png

    Steps 5 and 6: Paste and Tag

    Step 5 (paste): paste the code that was copied in step 2, to the red Dekiscript block under "Enter Dekiscript")

    Step 6 (save and tag): Save the page; and under page settings (expand the page setting) you will see a "Embed GLmol" option (see red arrow below), set it to "Yes".

    clipboard_edecb00903e64ce9c7ca25c128d2f925f.png

     

    Step 7: Refresh

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