[cctbxbb] Error in fractional coordinates returned by cctbx

[Petrus H Zwart]

Hi Andrew, 

I guess what happens is this:

When you use the expand_to_p1() command, the symmetry operators for P 32 2 1 are applied on the fractional coordniates as given. You expect a mod(1) operator to be carried out as well.

The advantage of not applying this operator is that you do not loose 'connectivity' between atoms.
I can imagine that this is not a real issue for certain inorganic compounds, but for organic compounds and proteins not having the 'intuitive' connectivity in the coordinates (atoms close to each other are bonded) this is an issue.

I agree with Eric that the negative fractional do not fit in your view of a perfect world view either.

I guess Ralf/the cctbx has something somewhere to do the mod(1) operation to get the fractional coordinates in the range you like. 

HTH

Peter



 








----- Original Message -----
From: David A Carr <dcarr2 at gmu.edu>
Date: Thursday, December 28, 2006 10:59 am
Subject: [cctbxbb] Error in fractional coordinates returned by cctbx
To: cctbxbb at phenix-online.org

> 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()
> 
>