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Combine Integrated Data Sources for Accurate Molecular Renderings
Display every atom in a protein with ProteinData, using accurate atomic radii from ElementData and built-in atom colors from ColorData.
In[1]:=

Click for copyable input
With[

 {p = "CD2AP", cr = Dispatch@ColorData["Atoms", "ColorRules"]},

 Graphics3D[

  MapThread[{#2 /. cr, 

     Sphere[#1, ElementData[#2, "AtomicRadius"]]} &, {ProteinData[p, 

     "AtomPositions"], Flatten[ProteinData[p, "AtomTypes"]]}], 

  Boxed -> False]

 ]
Out[1]=