[cctbxbb] unexpected behaviour of unit_cell.fractionalize

Jan Marten Simons marten at xtal.rwth-aachen.de
Wed Feb 13 07:17:45 PST 2013


When I try to convert a list of direct space coordinates into fractional 
coordinates like this:

from cctbx import xray
from cctbx import crystal
from cctbx.array_family import flex

structure = xray.structure(
      unit_cell=(3.14098, 4.08327, 5.33966, 83, 109, 129),

sites = flex.vec3_double( ((0.0, 0.1, 0.2), (1.3, 3.0, 2.3), (5.3, 0.1, 7.3)) )
sites_frac = structure.unit_cell().fractionalize(sites)

Now this returns a list of coordinates where x,y,z may be outside ot the 
interval [0,1[. ... quite unexpected.

It would be very nice to have at least an option like "restrict_to_asu" in 
unit_cell.fractionalize which would enforce (x,y,z) to be inside the 
asymmetric unit and/or "restrict_to_cell" which would enforce (x,y,z) to be 
inside the unit cell.

Could any of you more into the inner workings of the cctbx add this 
functionality, please?

Thanks in advance,


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