3D Presentation of Structural and Image Data

    Open AccessPublished:August 07, 2009DOI:
        Want to be the first on your block to include three-dimensional representations of structural or image data in your publication? It is now possible to create PDF documents with 3D images for submission as supplemental material with your Journal of Biological Chemistry (JBC) paper.
        Adobe has released Adobe Acrobat 9 Pro Extended for $82 (educational discount) or for a 30-day free trial. Visit the Adobe Page at With this program you can capture data from various 3D file formats and create a PDF suitable for publication in JBC as supplemental data (see steps below). We hope you will consider adopting this methodology for 3D images as it will enhance your presentation to convey more structural and image details as well as increase usefulness for readers. To facilitate the adoption of these techniques, we have created a video tutorial in the preparation of image files and import into PDFs for publication.
        We thank JBC Editorial Board member Martin Lawrence, Montana State University, for bringing this development to our attention and assisting in the preparation of the tutorial. Below are the suggested methods for embedding 3D PDFs.

        One-step for VRML2 Files (.wrl)

        • 1) Open Acrobat 9 Pro Extended
        • 2) Drag and drop the VRML2 file (.wrl) onto the Acrobat screen

        VRML2 Files (.wrl) Option 2

        • 1) Open Acrobat 9 Pro Extended
        • 2) File/Create PDF/From 3D Capture
        • 3) Start PyMol by double clicking on a PyMol script file (.pml) to generate the desired model (through Explorer)
        • 4) Then make the /Open the .wrl file

        For Other File Types (See Video for Demonstration)

        • 1) Open Acrobat 9 Pro Extended
        • 2) Launch PyMol via a PyMol script file to generate the desired model
        • 3) In Acrobat, select: File/Create PDF/From 3D Capture
        • 4) In the pop-up box, go to settings and check that 3D capture is enabled for PyMol, then hit OK
        • 5) Hit the Print Screen key from the keyboard (Shift/Print Screen)
        • 6) Choose Visualization/High Quality in the 3D conversion settings pop-up box, hit OK
        • 7) Hit OK again, if asked
        • 8) This process could be followed for other molecular graphics programs that don’t yet write VRML2 files
        For additional background and other information see Kumar et al. (Kumar, P., Ziegler, A., Ziegler, J., Uchanska-Ziegler, B., and Ziegler, A. (2008) Trends Biochem. Sci. 33, 408–412).