[cctbxbb] Error in fractional coordinates returned by cctbx

[Erik Mckee]

Perhaps I am misunderstanding something here, but aren't the negative
coordinates also outside the unit cell in your expectations?

On Thu, 28 Dec 2006, David A Carr wrote:

> 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()
>
>