Evan Nagata’s March 4th Update

This semester my project is to embed 3D chemical structures into a PDF so that they have full movement capabilities. I am working with Dr. Khuong and the ultimate goal is to use the 20+ PDFs to replace the Spartan program currently in use by the Biology Lab students to view chemical structures in a fluid 3D environment.

Alright, so over the past few weeks I’ve been working on constructing 3D models, and transforming them into a PDF format. The process involves using a couple freeware programs (OpenBabel and Chemsketch) as well as Adobe Acrobat. I got started with OpenBabel and Chemsketch pretty quickly for they were easiliy accessible and were relatively easy to work with. Chemsketch is the program in which the 3D chemical structure is actually created (and has a viewer in which you may move the object as you like). OpenBabel is a program that is used to convert file formats, and in this process, it will convert the Chemsketch .mol format to a .pdb (protein data bank) a format which Adobe Acrobat’s 3D toolkit recognizes which can then be used to eventually convert into PDF format.

For a short period of time, I was under the impression this 3D toolkit was an actual Adobe product for the way in which the tutorial for this process describes it as well as how Adobe describes it. However, upon further digging in attempt to find this toolkit, it became apparent it was an extension of Adobe Acrobat originally called the 3D toolkit, but in more recent versions (starting at version 9) is now called 3D reviewer.

Currently, I have reviewed the various documents that describe this process for 3D embedding in great detail, and have created a couple test molecules using Chemsketch which I then converted using OpenBabel. By tomorrow, what I am hoping to accomplish is to use Adobe Acrobat to successfully convert the .pdb file into a PDF.


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