On 8/22/12 6:06 AM, unverdor@biochem.mpg.de wrote: > we just stumbled across the same problem Ben had last year: > > get_transformation_aligning_first_to_second doesn't give the correct > results. Can the resulting transformation be applied with > get_transformed, like in the example?
Sure. You can also check the test case in modules/algebra/test/test_geom_alignment.py. It's possible that in pathological cases it's unable to improve the RMSD though.
Ben