Hi Allan, I'm not entirely sure why the difference between observed (experimentally measured) and calculated (using your script below) amplitudes of structure factors surprises you.. Also: - your script computes structure factors and prints out amplitudes (not intensities); - you do not set the B-factor. By default scatterer object is constructed with u_iso=0. Pavel On 8/24/15 15:01, Allan Lyckegaard wrote:
Dear CCTBX-list
I am trying to reproduce the (scaled) intensities for Si reported here: http://rruff.geo.arizona.edu/AMS/xtal_data/DIFfiles/15285.txt based on this information: http://rruff.geo.arizona.edu/AMS/CIF_text_files/15285_cif.txt
I am using CCTBX in Python:
from cctbx.array_family import flex
from cctbx import sgtbx, crystal, miller, xray
sgnum = 227
sg = sgtbx.space_group_info(sgnum).group()
latticepar = [5.43070, 5.43070, 5.43070, 90, 90, 90]
dmin = 1.0
atompos = [['Si',(0.0, 0.0, 0.0)]]
scatterers = flex.xray_scatterer()
scatterers.append(xray.scatterer(label=atompos[0][0], site=atompos[0][1]))
pg = sg.build_derived_point_group()
sym = crystal.symmetry(space_group=sg,unit_cell=latticepar)
sps = crystal.special_position_settings(crystal_symmetry=sym)
structure = xray.structure(special_position_settings=sps,scatterers=scatterers)
F = structure.structure_factors(d_min=dmin,algorithm='direct').f_calc()
list(F.amplitudes())
This gives:
[((0, 2, 2), 0.0),
((0, 4, 0), 120.21765812638594),
((1, 1, 1), 84.18849550806966),
((1, 3, 1), 65.48371727205928),
((1, 3, 3), 57.45438308324155),
((1, 5, 1), 51.48759686950681),
((2, 2, 2), 128.54540698861973),
((2, 4, 2), 0.0),
((3, 3, 3), 51.48759686950681)]
How come CCTBX give an amplitude of 0.0 for (0,2,2) and (2,4,2)? The measured intensities in the DIFfile above does not show this. Am I missing something?
Cheers, /Allan
_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb