Just for the record, except for charge density studies most small molecule
structures are refined with neutral atom scattering factors even when ions such
as Cl- are present. For example SHELX uses "4 Gaussian plus const: International 
Tables for Crystallography (1992)". Users rarely input ionic scattering factors
rather than using the default neutral atom scattering factors, possibly they are
afraid of a Category A Alert from CheckCIF if they have a charged crystal. In
practice, the difference between ionic and neutral atom scattering factors is 
mostly absorbed by the displacement parameters (B-values) and the R-factors are 
very similar. The main reason why routine small molecule R-values are rarely much 
less than 2% is the assumption that the scattering factors are spherically 
symmetrical, i.e. bonding and lone-pair electrons are ignored. This could be 
addressed by the inclusion of invarioms (precalculated aspherical scattering 
factors that depend on the local chemical environment of an atom) in Refmac and 
Phenix Refine.

George

On Wed, Nov 02, 2011 at 08:39:51PM -0700, Pavel Afonine wrote:
> Continuing on the subject, as far as I know there are at least three flavors of
>  form-factors currently used in refinement programs:
> 
> "4 gaussian plus const":
> International Tables for Crystallography (1992)
> 
> "5 gaussian plus const":
> D. Waasmaier & A. Kirfel. Acta Cryst. (1995). A51, 416-431. "New analytical
> scattering-factor functions for free atoms and ions"
> 
> "n-gaussian" (n determined dynamically)
> Grosse-Kunstleve RW, Sauter NK & Adams PD. Newsletter of the IUCr Commission on
> Crystallographic Computing 2004, 3:22-31. "cctbx news"
> 
> All three are available in PHENIX (the 3rd is used by default), and I presume
> the first one is used in CNS and Refmac, if I remember correctly (the authors
> of respective programs please correct me).
> 
> Pavel
> 
> On Wed, Nov 2, 2011 at 7:17 PM, Ivan Shabalin <[log in to unmask]> wrote:
> 
>     Hi James!
> 
>     Thank you very much for the gnuplot-ish version of ${CLIBD}/atomsf.lib!! It
>     works very nice and is very useful for education!
> 
>     As I understand, the form factor is the Fourier transform of electron
>     charge density. It is plotted as f(electrons) vs sin(tetta)/lambda and is
>     approximated as 5 Gaussian (Cromer and Mann) in REFMAC. And you made
>     reverse Fourier transform of the approximation and plotted the electron
>     density distribution in the real space.
> 
>     So, can I ask, what unit is x? Is it angstrom?
>     And what is Y? is it e/A3 (electron density)?
> 
>     I found, that at Bf=20, density profiles look almost the same for ions and
>     atoms (Mg2+ and Mg, Cl- and Cl). Does that means, there is no sense to
>     specify atomic charge in refmac refinement? It looks a bit strange, because
>     the numbers of electrons are different. Or decreasing in number of
>     electrons is compensated with significant decrease in atom size (that can
>     have the same effect as Bf lowering)? With Bf=0 the difference in curves is
>     significant.
> 
>     With best regards,
>     Ivan Shabalin
> 
> 

-- 
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582