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