Molecule is a utility MaxScript for 3DS Max 8/9 to create and render molecular models. (It may work for previous versions but I have not checked it on those.)
It allows you to import either Protein Data Bank Molecule data files. Or MOL data files.

The Molecule package also includes a material editor application with which you can assign specific colors to each atom substance in your molecules so the relationship of the different compounds are evident in the resulting model.

The Molecule package consists of the MaxScript. (.mse)
The Material Editor Application. (.exe) Integrated Help File. (.hlp) Which covers the importer and the editor.
Sample PDB & MOL Files and Sample Material assignemnt files (.mmf)

Please note: In some cases you will find that some PDB files from different sources on the web are malformed or just plain wrong in the outputted PDB format. Molecule is designed to operate with files which strictly adhere to the published accepted format for PDB data files.

11/25/2006 - Version 1.1
Changes & Additions:
              Loading and Saving of Presets added[Importer]
              Code optimizations [Editor & Importer]
              PDB / MOL malformed data optimizations
              Camera AutoPlace tweaked [Importer]
              Camera Lighting added [Importer]
              File Selection: Filename only is displayed [Importer]
                                      (Fixes long path visibity problems)
             Cancelling a file operation no longer throws an error [Importer]

2/13/2007 - Version 1.2
Changes & Additions:
             Lighting Multiplier control. Sets the multiplier for all active lights.
             Replaced Camera Activation checkbox with checkbutton
             Camera FOV - On settings import displays correctly
             Settings File now contains version info and version checking is enabled
             Sorry as I add features and add them to the settings file the old settings files
             become incompatable. The version checking allows a graceful exit.

3/xx/2008 - Version 2.0
Version 1.3 will not be released.
Molecule is being massively rewritten and will now be promoted to a full version release.
Version 2 will still retain the same functions, the camera and Lighting functions have had a
massive restructuring. The interface has been restructured to allow for additional functions
being added.
Problems with the the placement and targeting of the Light(s)
and Camera(s) should be eliminated.

Release date is as yet unknown but will be announced here and also at the
"ScriptSpot" and "HighEnd3D" sites

V2.0 Changes & Additions:
            Bi-Directional Bonds are now implemented. Bonds take the color of the
            originating atom.
            Model and Stats information is now able to be saved.
            Materials/Image Map usage has been improved.
            Support for importing Virtual Nano Lab Molecule scripts CANCELLED