Somewhere there will be a line which represents your placeholder, looking like this:
<img src="yourpicture.jpg" width="a number" height="a number">
Simply
change "img" to "embed",
and change the filename to reflect your PDB file!
<embed
src="yourfile.pdb" width="a number" height="a number">
Bait and Switch!
Create your document, placing a picture where you want a molecule. Be sure to size it properly - it doesn't matter if you distort your image to funhouse-mirror proportions, as it will be removed from the code in no time! Fire up notepad, locate your document, and open it up.