Unfortunately cn3d won't run without some additional software called Quartz...
|XQuartz-2.7.11.dmg||2.7.11||2016-10-29||For OS X 10.6.3 or later|
Find XQuartz-2.7.11.dmg, double-click, find XQuartz.pkg, double click. Click yes or continue as needed. Ignore the bit about needing to log out.
Download cn3d from ftp://ftp.ncbi.nlm.nih.gov/cn3d/Cn3D-4.3.1-OSX.zip
Check Downloads folder for either cn3d or Cn3D-4.3.1-OSX.zip. if you see just the zip file, double-clck the zip file which unpacks cn3d. This is the App you are looking for.
Move cn3d app from Downloads to Applicatons folder so you can find it later. Open applications folder find cn3d, double click to launch. You may see this warning: