[gmx-developers] Regarding commit Implementation of WAXS/SAXS refinement in MD!

Alexander Björling alex.bjorling at gmail.com
Mon Oct 13 12:26:55 CEST 2014

> From: Anjaiah Nalaparaju <anjai.che at gmail.com>
> My question is related to the unmerged patch for module waxsdebye.
> 1. Can anybody tell the reference for the form factor
> coefficients(a1-a5,b1-b5,p1-p3) in file "sfactor_atom_nods_Fourier.xml" or
> all the new .xml files on sfactors. These number look very much different
> from the sfactor.dat which are cromer-mann coefficients.
There is no reference (yet). The numbers are different because it's a
different parametrization. Since solvent-corrected form factors have a more
complex shape, we've used a short Fourier sum plus a polynomial, instead of
gaussians. The form factor is calculated from these parameters in

> 2. If we use the following equation to calculate atomic form factors, at
> q=0  sum of co-eff a1 to a5 should be equal to the form factor value at q=0
> given in the publication "Niebling, Bj?rling and Westenhoff, J. Appl.
> Cryst. 47 (2014) 1190"
No they shouldn't, there's also a polynomial there. Again, see
scattering_factors.cpp. Have that code print out the scattering factors if
you would like to test them.

> [image: View the MathML source]
> But seems the coefficients in .xml files are not corresponding to this
> equation.
> 3. How can the coefficients after displaced volume correction can be a
> constant value ( sfactor_atom_ds_Fourier.xml), as the displaced volume
> correction term also function of "q". "Svergun, Barberato and Koch, J Appl.
> Cryst. 27 (1995) 768."
I'm not sure what you mean by "constant value".

> 3. Where the form-factors with displaced volume corrections are calculated
> in the code.
The displaced volume corrections are not done in the code. The scattering
factors with or without the correction (depending on which xml file is
used) are calculated in scattering_factors.cpp.
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