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This is what I get it to work.

  1. Run

/usr/libexec/java_home -V

  1. Identify version 8 of Java, and remove the others using a command like

rm -rf /Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/

(with the version suitably changed; also you'll probably have to run this as sudo)

It turns out that JMol is incompatible with version 9, which I originally had. After getting rid of version 9, closing the shell session and restarting it, I am now able to plot 3d objects in Sagemath through JMol.