Unfortunately cn3d won't run without some additional software called Quartz...

Download XQuartz prerequisite

DownloadVersionReleasedInfo
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 Download and install

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:

In macOS Catalina and macOS Mojave, when an app fails to install because it hasn’t been notarized or is from an unidentified developer, it will appear in System Preferences > Security & Privacy, under the General tab. Click Open Anyway to confirm your intent to open or install the app.

You are done!

cn3d should be ready to go!