Thanks, Bob. I will check the update.
This is what I found (with the old versions):
When the atom subset has in both models exactly the same relative
postitons (this is possible since they come from drawn formulas), the
RMSD calculated by "compare" is exactly zero. Then, the "rotate
translate" options produces the problem: the model being moved
disappears and Jmol gets unresponsive (there is still mouse
interaction but no commands may be issued, you need to quit the
application)
I found that by modifying slightly one of the coordinates in one of
the atoms involved in comparison (e.g. {atomNo=5}.atomX =
{atomNo=5}.atomX + 0.05), the problem goes away (and I can even
re-modify back the coordinate later, atomX = atomX - 0.05)
So that's a workaround for older versions (I cannot plug this updated
Jmol into MP right now).
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