[cctbxbb] Missing gaussians for some ions?

[Jan Marten Simons]

Hi,

I did some more tests using cif files from cod and found out that some of those 
trigger errors like this for http://www.crystallography.net/cif/1/1000029.cif:

Traceback (most recent call last):
  File "Check_F_calc.py", line 29, in <module>
    f_calc = structure.structure_factors(d_min=1.0).f_calc()
  File "/home/marten/Arbeit/cctbx-
latest/cctbx_sources/cctbx/xray/structure.py", line 813, in structure_factors
    algorithm=algorithm)
  File "/home/marten/Arbeit/cctbx-
latest/cctbx_sources/cctbx/xray/structure_factors/from_scatterers.py", line 
53, in __call__
    miller_set=miller_set)
  File "/home/marten/Arbeit/cctbx-
latest/cctbx_sources/cctbx/xray/structure_factors/from_scatterers_fft.py", line 
32, in __init__
    tolerance_positive_definite=manager.tolerance_positive_definite())
RuntimeError: gaussian not defined for scattering_type "Y4+".


The cif file itself can be read and gives a valid summary:

Number of scatterers: 13
At special positions: 5
Unit cell: (7.82927, 7.82927, 5.70757, 90, 90, 120)
Space group: P 3 1 c (No. 159)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
Y1   Y4+    2 ( 0.3333  0.6667  0.2420) 0.27 0.0000 [ - ]
Si1  Si4+   6 ( 0.5087  0.0819  0.2130) 0.77 0.0000 [ - ]
Al1  Al3+   6 ( 0.5087  0.0819  0.2130) 0.23 0.0000 [ - ]
Si2  Si4+   6 ( 0.1706  0.2533  0.0020) 0.77 0.0000 [ - ]
Al2  Al3+   6 ( 0.1706  0.2533  0.0020) 0.23 0.0000 [ - ]
N1   N3-    2 ( 0.0000  0.0000  0.0000) 0.94 0.0000 [ - ]
O1   O2-    2 ( 0.0000  0.0000  0.0000) 0.06 0.0000 [ - ]
N2   N3-    2 ( 0.3333  0.6667  0.6530) 0.94 0.0000 [ - ]
O2   O2-    2 ( 0.3333  0.6667  0.6530) 0.06 0.0000 [ - ]
N3   N3-    6 ( 0.3458 -0.0472 -0.0050) 0.94 0.0000 [ - ]
O3   O2-    6 ( 0.3458 -0.0472 -0.0050) 0.06 0.0000 [ - ]
N4   N3-    6 ( 0.3219  0.3180  0.2460) 0.94 0.0000 [ - ]
O4   O2-    6 ( 0.3219  0.3180  0.2460) 0.06 0.0000 [ - ]
Y1:   0.3333   0.6667   0.2420
  point group type: 3
  special position operator: 1/3,2/3,z
Si1:   0.5087   0.0819   0.2130
  point group type: 1
  special position operator: x,y,z
Al1:   0.5087   0.0819   0.2130
  point group type: 1
  special position operator: x,y,z
Si2:   0.1706   0.2533   0.0020
  point group type: 1
  special position operator: x,y,z
Al2:   0.1706   0.2533   0.0020
  point group type: 1
  special position operator: x,y,z
N1:   0.0000   0.0000   0.0000
  point group type: 3
  special position operator: 0,0,z
O1:   0.0000   0.0000   0.0000
  point group type: 3
  special position operator: 0,0,z
N2:   0.3333   0.6667   0.6530
  point group type: 3
  special position operator: 1/3,2/3,z
O2:   0.3333   0.6667   0.6530
  point group type: 3
  special position operator: 1/3,2/3,z
N3:   0.3458  -0.0472  -0.0050
  point group type: 1
  special position operator: x,y,z
O3:   0.3458  -0.0472  -0.0050
  point group type: 1
  special position operator: x,y,z
N4:   0.3219   0.3180   0.2460
  point group type: 1
  special position operator: x,y,z
O4:   0.3219   0.3180   0.2460
  point group type: 1
  special position operator: x,y,z

Other cif files give other missing gaussians:

http://www.crystallography.net/cif/1/1000145.cif:
> RuntimeError: gaussian not defined for scattering_type "V4+".

http://www.crystallography.net/cif/1/1000181.cif:
> RuntimeError: gaussian not defined for scattering_type "H1+".

http://www.crystallography.net/cif/1/1000353.cif:
> RuntimeError: gaussian not defined for scattering_type "H1+".

I'm not sure if this is a problem related to the notation used in those cif 
files or if cctbx is missing some data here that should be added to it.


With regards,

 Dipl. Pyhs.
  Jan M. Simons
 
Institute of Crystallography
RWTH Aachen University