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1. Does anyone know of a program that will calculate structure factors
using U (anisotropic B factors) from a model?  This doesn't look to be do
difficult modification for me to make if I can't find one, but then I'd
have a hard time figuring out how to validate that it was working
properly.
shelx, GSAS, cctbx, [etc most program in the small molecule world]

Easy to put in for triclinic cells - endless fun to be had with symmetry constraints for general space groups (eg: try to find a program that does hexagonal space groups in a C-centred orthorhombic setting)

2. Does anyone have a formula or defination for epsilon (statistical
weight/symmetry attribute of a lattice point)?
Number of times the lattice point is transformed into itself by the rotational part of symmetry operators of the space group, with the translational part modulo 1 as zero (otherwise it's absent). See:
http://www.iucr.org/iucr-org/comm/cteach/pamphlets/9/9.html

-Jon


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