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 <shabali...@inbox.ru> 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
>
