File formats/3D PDF

PDF documents with integrated 3D interactive models

Easy procedure

This is currently the easiest way to create a PDF document containing an interactive 3D molecular model, using only free software (at least free in Windows; solutions for the Mac need more investigation to confirm).

Downloads

• Windows and MacOS: download the graphic user interface version of IDTFConverter from the Jmol website:
  • Windows: download the IDTF_U3D_Converter.zip, unpack the zip file and put the single IDTF_U3D_Converter.exe file wherever you want in your local disk. If you find it convenient, create a shortcut for it in the desktop or the Start menu.
  • MacOS: choose and download the app suitable for your system:
    • IDTF_U3D_Converter_Intel.zip if your computer is based on an Intel processor. Unpack the zip file to obtain the executable file, IDTF_U3D_Converter.app
    • IDTF_U3D_Converter_Silicon.zip if your computer is based on a Silicon processor (usually ARM). Unpack the zip file to obtain the executable file, IDTF_U3D_Converter.app

Create the IDTF file

1. Get a current version of Jmol application. Open your molecule; display it in the desired orientation and style.
   • Suggestion: make the Jmol window square, using top menu > Display > Resize and entering two equal numbers. The result will look better if you insert it later into a square box within the pdf.
   • Note: you can also do it with JSmol embedded in some webpage. Generation of the idtf file may take longer, though, if the model is complex.
2. If the export to IDTF option has been implemented in the menu:
   • Top menu bar > File > Export > Export to IDTF
   • Pop-up context menu > File > Export > Export IDTF 3D model
3. Otherwise, open the console and enter write myMol.idtf
4. Two files will be created: myMol.idtf and myMol.idtf.tex. For the current method, you may discard the .tex file.

Create the U3D file

• Open the IDTF_U3D_Converter program or app, browse to load your .idtf file, choose the output folder and click on "Convert". The output will have the same filename as the input, with extension .u3d

Prepare your PDF document

1. Use your preferred program (word processor, presentation, ...) to create a document with text and images, leaving square space(s) where you will later insert the 3D molecular models, and export to pdf format.
   • If your application cannot export to PDF directly, you may use a virtual PDF printer like PDFforge PDF Creator or PDF-XChange Lite Printer (both available for free).
2. To insert the 3D models you need a pdf editor that is compatible with the 3D-PDF standard. Examples: Adobe Acrobat Pro and PDF-XChange Editor (Windows-only, free or paid version)
3. In PDF-XChange Editor: open the previous PDF, find the place where your left blank space. To insert a 3D annotation there:
   • If you are using the Ribbon interface: Comment > Add 3D
   • If you are using the classical Toolbar interface: Tools > Media tools > Add or edit 3D annotations
   • Draw the rectangle area with the mouse. Suggestion: draw a square by holding the Shift key while dragging to define the area.
   • In 3D Artwork, select your myMol.u3d file.
   • Choose among any other display options offered (like activation of the content, border and background color)
   • Accept and save the file.
4. In Adobe Acrobat Pro: open the previous PDF, find the place where your left a blank space. To insert 3D media there:
   • From the upper left of the screen, select All tools > Add rich media > 3D media.
   • Drag a rectangle (better, a square) to define the area for the 3D model. An Insert 3D dialog box appears.
   • In the Insert 3D dialog box, browse to select your myMol.u3d file. Check Show Advanced Options to set the initial properties.
   • Adobe help for this procedure.

Viewing the result

• Check the 3D display in a PDF viewer application. Note that not all viewers support this kind of 3D content.
  • The pdf viewers implemented internally in web browsers do not currently support 3D objects and will just display a static image.
  • Adobe Acrobat Pro and the free Adobe Reader support 3D objects.
  • PDF-XChange Editor supports 3D objects.
  • Recent versions of Foxit PDF Reader support 3D objects. Display of 3D objects may be disabled by default. You may enable it either by trusting the document or by setting: File > Preferences > 3D > Enable the playing of 3D content.
• In Android devices you may use '3D PDF Viewer' or possibly other apps (search the Google Play store).
• In iOS devices you may use '3D PDF Viewer' (search the App Store) or possibly other apps. This may also be run in a Mac computer.

Sample documents

These have been created following the above procedure

• Cysteine
• Alanine
• Coagulation Factor Xa

Note the model will not display as 3D and interactive if you view it inside the web browser; you need to download the file and open it in a compatible PDF viewer.

Older reference

This old content may or not be currently useful, but it is kept for the record at File_formats/3D_PDF/Legacy

Contributors

AngelHerraez, Vdlee