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

[Alexander Björling]

> 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
src/gromacs/waxsdebye/scattering_factors.cpp.


>
> 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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