[cctbxbb] Structure factor calculation weirdness

[Oleg Dolomanov]

Hi Graeme,
indeed, by setting d_min you modify the miller set which is used to calculate the structure factors,
Cheers,
o

From: Graeme.Winter at diamond.ac.uk
To: cctbxbb at phenix-online.org
Date: Fri, 7 Dec 2012 15:36:42 +0000
Subject: [cctbxbb] Structure factor calculation weirdness









Hi Folks,
 
Some confusion here at diamond – it seems that the amplitude of F(hkl) depends on dmin
 
----------------
 
from cctbx import xray
from cctbx import crystal
from cctbx.array_family import flex
 
# 14keV
 
wavelength = 12.3984 / 14.0
 
spgroup = 'Fd-3m'
latt = (5.4309, 5.4309, 5.4309, 90, 90, 90)
atoms = [('Si', 0.125, 0.125, 0.125)]
 
allscatterers=[]
for atom in atoms:
    allscatterers.append(xray.scatterer(
        label = atom[0],
        site = (atom[1], atom[2], atom[3]), u = 0))
 
structure = xray.structure(
    special_position_settings = crystal.special_position_settings(
    crystal_symmetry = crystal.symmetry(
    unit_cell = latt,
    space_group_symbol = spgroup)),
    scatterers = flex.xray_scatterer(allscatterers)).expand_to_p1()

 
for dmin in 5.0, 2.5, 1.7:
 
    print dmin
    f_calculations = structure.structure_factors(
        d_min = dmin).f_calc().amplitudes().show_array()
 
---------------
 
Chopped out only 001, 010, 100 from this…
 
5.0
(0, 0, 1) 0.290277589693
(0, 1, 0) 0.290277589693
(1, 0, 0) 0.290277589693
2.5
(0, 0, 1) 0.0
(0, 1, 0) 0.0
(1, 0, 0) 0.0
<snip>
1.7
(0, 0, 1) 0.278378587828
(0, 1, 0) 0.278378587828
(1, 0, 0) 0.278378587828
<snip>
 
Have we misunderstood something?
 
Thanks,
 
Graeme
 
Dr. Graeme Winter
Senior Software Scientist
Diamond Light Source
 
+44 1235 778091 (work)
+44 7786 662784 (work mobile)
 
 



 

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