[cctbxbb] Missing gaussians for some ions?

Jan Marten Simons marten at xtal.rwth-aachen.de
Thu Dec 23 12:30:50 PST 2010

Am Donnerstag 23 Dezember 2010 17:06:00 schrieb Ralf W. Grosse-Kunstleve:
> Hi Jan,
> > So, do I have to edit/patch cctbx/xray/structure.py: to  achieve the
> > desired behaviour
> Yes, just to test if it does what you need.

Ok, after this change those cif files can be used to calculate f and d values 
as well.

As far as I understand the code (in /eltbx/xray_scattering.h) setting 
exact=False leads to using the form factor of the bare atom from the form 
factor coefficient table, so in case an ion is in the table it will still be 
using the optimised form factor for this, right?

> > or is there a better way?
> > (Imho best way would  be to have more
> > optional parameters for  structure.structure_factors().f_calc().)
> It would fit better to expose the "exact" setting as an optional
> parameter of xray.structure.scattering_type_registry(), under
> some more telling name, maybe "exact_table_lookup".
> The idea is that you call this method before doing any structure
> factor calculations if the settings need to be customized. The last
> explicit call determines the state of the registry. (I know
> this mechanism isn't obvious, but I was trying to avoid introducing
> even deeper object hierarchies.)

That mechanism would definatly need some documentation then (with a hit to the 
docs in structure.structure_factors() docstring [1]).

I'm willing to work on inducing verbose docstrings to the python interface 
(after xmas break), i'f you're OK with this.

[1] http://tovid.wikia.com/wiki/Python_tips/Docstrings

With regards,

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

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