It seems that "rotate" cancels the spin
I have no clue if this has ever been by design.
You could apply a fix by reading the spinning state before doing the rotate
and reapplying it later:
Jmol.jmolCheckbox(myJmol,
"reset;",
"ss = _spinning; reset; rotate x 90; if (ss) { spin on; }",
" Base-stacking");
And why do you have in your spin checkbox those complex commands?
Jmol.jmolCheckbox(myJmol, "spin off; spin on;", "spin on; spin off;",
" Spin", true);
I would just do
Jmol.jmolCheckbox(myJmol, "spin on;", "spin off;", " Spin", true);
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