The compare command appears to align atoms correctly -- that is, it appears to
give the same results as Chimera.
The RMSD it reports in the Java console, however, does not match my
calculations (which do match Chimera!). I haven't been able to figure out what
Jmol _is_ reporting, but I'm hoping someone (OK, Bob) can add this to his to-do
list.
Thanks!
--Dan
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