[cctbxbb] Best way to compare two structures using cctbx?

[Jan Marten Simons]

Hi,

I think I've seen some code in cctbx which tries to put the similarity of two 
crystal structures into a number. Am I right on this?

I want to have something similar:

I'm interested in comparing the direct space atomic distances of two 
structures sharing the same unit cell parameters and space group and 
scatterers but different atomic coordinates for those. Now I'd like to have a 
mapping where I could compare the bond lengths between all scatterers which 
should eliminate any movements which might also be due to a shift in the 
origin of a P 1 cell. Also I'd like to have a value for mean, minimal and 
maximal displacements.
The purpose of this is to check how good a structure approximation matches a 
reference structure.

How would you suggest to take on this task? Or is there even some code related 
to this?

Thanks in advance,

Jan