[cctbxbb] Error in fractional coordinates returned by cctbx

[David A Carr]

Hello,

I have encountered the following inconsistency when working with cctbx.  The compound I am working with is as follows.

#Silicon Dioxide Quartz low.
#Si O2
#ICSD Coll Number 62410

label="Si", site=(0.4643,0.0,0.6667)
label="O", site=(0.411,0.2773,0.7783)

unit_cell="4.8430, 4.8430, 5.3480, 90.0, 90.0, 120.0",

space_group_symbol="P 32 2 1"



The error is can be seen in the below.  In the second and third Si lines the z value is not a fraction of the unit. Similarly two of the oxygens are placed outside the unit cell.  Why does cctbx place these outside of the unit cell?   

Number of scatterers: 9
At special positions: 0
Unit cell: (4.843, 4.843, 5.348, 90, 90, 120)
Space group: P 1 (No. 1)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
Si1  Si     1 ( 0.4643  0.0000  0.6667) 1.00 0.0000
Si1  Si     1 ( 0.0000  0.4643  1.3333) 1.00 0.0000
Si1  Si     1 (-0.4643 -0.4643  1.0000) 1.00 0.0000
O1   O      1 ( 0.4110  0.2773  0.7783) 1.00 0.0000
O1   O      1 (-0.2773  0.1337  1.4450) 1.00 0.0000
O1   O      1 (-0.1337 -0.4110  1.1116) 1.00 0.0000
O1   O      1 ( 0.1337 -0.2773 -0.4450) 1.00 0.0000
O1   O      1 (-0.4110 -0.1337 -0.1116) 1.00 0.0000
O1   O      1 ( 0.2773  0.4110 -0.7783) 1.00 0.0000

Below shows the expected fractional coordinates as  expected.  Based on the space group P 32 2 1.

 0.4643  0.0000  0.6667
 0.0000  0.4643  0.3333
-0.4643 -0.4643  0.0000
 0.4110  0.2773  0.7783
-0.2773  0.1337  0.4450
-0.1337 -0.4110  0.1116
 0.1337 -0.2773 -0.4450
-0.4110 -0.1337 -0.1116
 0.2773  0.4110 -0.7783 

Any insight into this would be of help.  I am hoping to use cctbx as a part of our current software development project.


Thanks,

D.Andrew Carr
dcarr2 at gmu.edu


# Below is the code that generates the error
#  posted above.
#---------------------------------------------------
from cctbx import xray
from cctbx import crystal
from cctbx.array_family import flex

def demo():
  crystal_symmetry = crystal.symmetry(
    unit_cell="4.8430, 4.8430, 5.3480, 90.0, 90.0, 120.0",
    space_group_symbol="P 32 2 1")
  scatterers = flex.xray_scatterer()
  scatterers.append(xray.scatterer(
    label="Si", site=(0.4643,0.0,0.6667)))
  scatterers.append(xray.scatterer(
    label="O", site=(0.411,0.2773,0.7783)))
  icsd_structure = xray.structure(
    crystal_symmetry=crystal_symmetry,
    scatterers=scatterers)
  print "ICSD Structure"
  icsd_structure.show_summary().show_scatterers()
  print
  icsd_structure.show_distances(distance_cutoff=2.5)
  print "Primitive"
  primitive_structure = icsd_structure.primitive_setting()
  primitive_structure.show_summary().show_scatterers()
  print
  p1_structure = primitive_structure.expand_to_p1()
  p1_structure.show_summary().show_scatterers()
  print
  print "Expanded to P1"
  icsd_structure.expand_to_p1().show_summary().show_scatterers()
  print "OK"

if (__name__ == "__main__"):
  demo()

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