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3D Best Fit Alignments - "SCALING"

Trying to obtain some more information on "scaling" underneath the 3d best fit alignment on PCdmis? I have read the help section, but I am still a little unclear on how it works, should I use it, and if so when should I use it. I normally do most of my best fit jobs utilizing Axyz software, seems as if the algorithm gives me better results than the regular best fit on pcdmis. I am set up on a job that has 16 details that need to be best fit into a pattern relationship. These details encompass about 40" in width, 200" in length and roughly 50" in depth. When I do a best fit solution on Axyz I get about a .005 RMS solution which is well within my tolerance. When I perform the same solution in pcdmis I get a RMS of .0085, which is still in tolerance. If I then apply the scaling factor to the best fit my RMS drops from .0085 to .0061 which is closer to what I was getting using Axyz. Not for sure what the scaling is actually doing to my measurements. Dose anyone have any insight or know anyone that might be well versed in this area?