Hi,

For me IMP.em.FitRestraint is much slower with use_rigid_bodies = True, while the doc says it should be faster.

For example,
running imp/modules/em/test/expensive_test_resample_by_rigid_bodies.py test like this:
python -m unittest expensive_test_resample_by_rigid_bodies.Tests.test_resample
runs in ca. 3.3s

Now if I change the line 72:
self.all_ps_copy, map, [0., 0.], IMP.atom.Mass.get_mass_key(), 1, True)
to
self.all_ps_copy, map, [0., 0.], IMP.atom.Mass.get_mass_key(), 1, False)
(so setting use_rigid_bodies to False)
it runs in 0.6 seconds ...

It also always runs much slower with this option in my own scripts.

I think it has something to do with different resampling method when rbs are used.