Hi Eric
I agree it's a bug. I would expect both models to be saved, and the doc says
"Only the currently selected atoms are saved."
If you save to SDF it works as expected.

The fact that the file has MODEL ENDMDL means that Jmol is indeed 
intending to save both.

So for proteins, you could instead use
  write test.jmol
which works fine. Of course, that's a binary file (may be an issue if you want 
to work with local webpages).


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