Structural Biochemistry/Molecular Modeling/Interactive 3D Model within a PDF

Interactive 3D Model within a PDF (3D PDF) is a process by which a selected structural data is integrated into a 3D model within a PDF. This process allows a shortened learning curve to learning how to operate it, compared to the more well known software’s that are used to visualize structural data. On top of being user-friendlier, interactive 3D model within a PDF allows for a 3D model to be presented in any publications or writings, which allows for the reader to get a visual perspective on the molecule that they are reading about. The PDF version allows for an integration of other media, such as video and audio. The main advantage of 3D PDF is the ability of the reader to access 3D structures, while also being able to read the article at the same time [1].

Exporting Molecular Models in 3D into PDF formatEdit

Using PyMOL, which is a popular software tool used for molecular visualization, one can embed 3D images into PDF publications through the process of three steps: 1. Export components of the 3D model as a VRML2 files through the use of PyMOL. The file is in (.wrl) form. 2. Process the model components by commercial 3D software, which allows the user to get a U3D file, which comes with all of the parts of the 3D model. The file is in (.u3d) form. 3. In order to embed the U3D into a PDF file, one can use Adobe Acrobat 9 Pro Extended software suite in order to complete the process. [2]

Alternative ways to create a 3D PDFEdit

1. One alternative way to create a 3D PDF is to use the function of the Adobe Acrobat 9 Pro Extended, called “3D capture.” In this, the OpenGL graphics signal is captured. The PyMOL and Adobe Acrobat 9 Pro Extended are opened at the same time and the picture that is displayed in PyMOL is captured by the Adobe Acrobat 9 Pro Extended in a 3D form. After this the file is saved in the PDF form. The advantage to this is that the saved file can be edited and then saved as U3D file, which as pointed out before, is embedded into a PDF file that have all the proper settings, resulting in a 3D PDF model. The downside to this alternative way is that the models are much smaller compared to the original results from other procedures. [2]

2. Another alternative way to create a 3D PDF involves the LaTEX document preparation system. In this approach the LaTEX document preparation system is used with the movie 15 package. The Adobe Acrobat 9 Pro Extended creates files, either a U3D or a PRC file, which contain the 3D molecular models. These files are inputted and from that a PDF document is produced, containing the 3D image. The important part is that the LaTEX and movie 15 script for the integration of the models into the PDF file. [1]

3. A third alternative way to create a 3D PDF is called MeshLab. Using VRML2 files from PyMOL, MeshLab software turns these files into U3D format, which can be used to embed 3D images into PDF files using Adobe Acrobat 9 Pro Extended or the LaTEx/movie15. [1]

The different approaches for embedding interactive molecular models into PDF files

Existing Problems with 3D PDFEdit

1. Some online submission systems are unable to build the final PDF file using individual files. 2. There are submission systems that do not accept the 3D PDF format files. 3. File size of publication that contain interactive 3D images must be below 10 MB in order to be accessible.


1] Kumar, Pravin, Alexander Ziegler, Alexander Grahn, Chee Hee, and Andreas Ziegler. "Leaving the Structural Ivory Tower, Assisted by Interactive 3D PDF." PubMed. N.p., n.d. Web. 20 Nov. 2012. <>.

[2] Kumar, P. et al. (2008) Grasping molecular structures through publication-integrated 3D models. Trends Biochem. Sci. 33, 408–412