To watch this video you need “red-cyan anaglyph glasses”: en.wikipedia.org/wiki/Anaglyph_image#Viewing This video was made with Mathematica 7. This type of red-cyan anaglyph videos can be useful for display of complex 3D structures. Once the structure is built it takes just a few lines of Mathematica code to render a stereoscopic 3D tour of it. The actual code to produce the visual part is so short that I show it below for instructive purposes.

To read about the molecule visit proteopedia.org/wiki/index.php/1tf6

Mathematica package: StereoImagery.m by Mark Fisher, markfisher.net/~mefisher/

Soundtrack: "Impromptu in Quarter Comma Meantone", Kevin MacLeod, incompetech.com , Licensed under Creative Commons "Attribution 3.0" creativecommons.org/licenses/by/3.0/";

======== Mathematica CODE ========
Needs["StereoImagery`"]
IMG = Import["URL", "PDB", Background -> Black, Axes -> False];
FILMmol = Table[MakeAnaglyph[Show[IMG, ViewAngle -> 33 \[Degree], ViewPoint -> (.1 + Sin[t {1.062, 1.358, 1.566}]), ImageSize -> 1500]] , {t, .3, 3.7 Pi, .005}];
Export["FILMmol.avi", FILMmol]
======== Mathematica CODE ========

The code uses URL: rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&\compression=NO&structureId=1tf6

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