[cctbxbb] Missing gaussians for some ions?
Ralf W. Grosse-Kunstleve
rwgk at yahoo.com
Wed Dec 22 14:48:21 PST 2010
We have the N-Gaussians for all ions that appear in the International Tables
Volume C. You can find the source code for the compiled-in tables here:
> RuntimeError: gaussian not defined for scattering_type "Y4+".
> RuntimeError: gaussian not defined for scattering_type "V4+".
> RuntimeError: gaussian not defined for scattering_type "H1+".
These three do not appear in the Int. Tables. We'd need to find out what form
factors were actually used in the refinement. I see the structures are from
1981-1993. It could be very difficult to find out for sure.
We already have an option to make the form factor lookup less strict.
The critical line is this in cctbx/xray/structure.py:
std_lbl = eltbx.xray_scattering.get_standard_label(
label=t_undef, exact=True, optional=True)
I think your script should run if you set exact=False, but it will
use plain Y, V, H form factors for the unknown ions. Is that good
enough for your purposes?
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