Ah, I see what is happening, and it is certainly Jmol's oddity and a bug.
In Jmol,
rotate SELECTED <3x3 matrix> TRANSLATE <vector>
allows a model to be rotated around its center of geometry while it is
being translated -- an interesting effect, but not what is intended with
rotate SELECTED <4x4 matrix>
Fixed in next release.
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.11_2014.12.17.zip
Jmol.___JmolVersion="14.3.11_2014.12.17"
bug fix: rotate selected <4x4 matrix> should not rotate about center of
atoms
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