Incorporating VRML molecular images in Powerpoint presentations

 

Background

 

VRML files allow real-time manipulation of graphic objects, and since some molecular modeling and rendering programs provide for VRML output, there is the opportunity to have presentations that permit real-time manipulations of these objects. Powerpoint is a commonly used program for seminars, and the question arises as to how to incorporate VRML files of molecular objects into Powerpoint presentations. After much time and anguish, I have identified all the relevant programs and utilities to allow the incorporation of VRML files into Powerpoint presentations. Here is how to do it:

 

1. Producing a VRML file from a PDB file (e.g. protein structure)

 

Not many PDB modeling or rendering programs provide for VRML output; one program that does is DS Visualizer by Accelrys. This program will allow you to read in a PDB file and render ribbon drawings, spacefilling atom representations, etc. and save in VRML format. This is (was) a free version that can be downloaded from:

 

http://accelrys.com/products/discovery-studio/visualization/discovery-studio-visualizer.html

 

The VRML output from this program is in VRML1.0 format. With regard to plug-ins to view VRML files in Powerpoint, the most reliable ones I have found work best with VRML2.0 files. This brings us to the next point:

 

2. Converting VRML1.0 to VRML2.0 formats

 

There are a few converters available to permit reading VRML1.0 files and writing VRML2.0 files. Unfortunately, most of the ones I tried did not work well (i.e. did not faithfully convert colors, etc.). In fact, I only found one that worked well:

 

cp_vrml1to2.zip

 

This zipped file contains two files: a command line executable and a DDL file. Unzip the files and place in a working directory. Open a command window and give the command for the executable as follows:

 

vrml1tovrml2.exe "input filename" > "output filename" (don't use the actual quotation marks; do use the redirection symbol between the filenames - otherwise the output file will go to the screen only).

 

3. Installing a VRML plugin for Powerpoint

 

Again, there are a couple of these plugins available, however, not many seem to work reliably. Many seem to have real problems with the lighting (i.e. "headlight" command) and produce a very dim image. I found one that worked great, but would not retain the name of the VRML file upon closing powerpoint. One that does work well is the Cortona viewer from ParallelGraphics:

 

http://www.parallelgraphics.com/products/cortona/

 

Once installed you can give the "insert object" command in Powerpoint and one of the listed objects will be "ParallelGraphics Cortona Control". Insert this object, right click it, select "Properties" and a window will open with a list of options. Select "Scene", click the "" button and browse for the VRML file to be inserted. Close the options window and view the Powerpoint slide (as slideshow). The VRML object can now be manipulated within the Powerpoint presentation!

 

One final issue relates to the path for the VRML file and transferring the Powerpoint presentation to another computer (e.g. laptop). The location of the VRML file in the "Scene" parameter will have a format of "file//driveletter:/foldername(s)/filename". This will be true even if you just type the filename (and it is in the local directory). Thus, you need to be sure the drive and folder names/structure is identical between computers (or edit the presentation on the new computer to identify the new location for the VRML files).

 

Final Notes

 

If you right click on the VRML window during a slide show in Powerpoint, you will bring up the "Preferences" dialog box. If you click "Skin" and then select "CAD", an extremely useful set of buttons will be displayed that is most appropriate for manipulating molecules.

 

 

Dr. Michael Blaber 2003