UCSF has a respected molecular biology department and as a product of their research, they've released to the public (several years ago) a program that enables you to visually turn and handle molecules. I remember using this program as an undergrad.
The name of this program is called Chimera. You can use this to illustrate the complex molecules that our bodies produce or to illustrate the shape and dimensions of proteins, enzymes, DNA and even RNA.
Using Chimera has a moderate learning curve, however, since you must familiarize yourself to use these funky file types (PDB files and 4 character file names). There are lots of databases you can use to get these files, but I like to use the Research Collaboratory for Structural Bioinformatics Protein Databank.
So using the databank mean as you type in a protein of interest, say "human type III collagen" or 3MDW. They'll give you list of search results and you can download a PDB file that can be opened and viewed through Chimera.
The link has been added to Biology as Program - Chimera Molecular Models.
Enjoy and good luck!
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