[gmx-developers] Regarding commit Implementation of WAXS/SAXS refinement in MD!
Anjaiah Nalaparaju
anjai.che at gmail.com
Tue Oct 14 06:38:24 CEST 2014
Hi,
I understood the coefficients in .xml file. There is a coefficient "a0",
this is taking care of formfactor value at q=0.
Best regards
On Mon, Oct 13, 2014 at 10:03 PM, Anjaiah Nalaparaju <anjai.che at gmail.com>
wrote:
> Thank you for providing a detailed explanation.
>
> Actually I should focus only on asking about all atom form factors table
> which is " sfactor_atom_nods_Fourier.xml ". In this there is no solvent
> displaced correction so we no need to use any polynomial correction. I
> suppose the coefficients in these table should be close to the cromer-mann
> coefficients (from quantum calculations) or to be in a form to use in the
> following equation to calculate atomic form factor.
> [image: Inline image 1]
>
> As I can see the coefficients given in the .xml file are very different I
> would like to know what is the equation used to calculate atomic form
> factor. In principle, whatever the method or coefficients we use the atomic
> factor at q=0 will be equal to atom number. I am not clear how this is
> satisfied from your coefficients given in " sfactor_atom_nods_Fourier.xml
> ". For example for atom "Carbon" I expect sum of a1 to a5 should be equal
> to 6.
>
> Please correct me if I have mistaken any concept in your implementation.
>
> Thanks for your time and kind help.
> Best regards
>
>
>
>
> On Mon, Oct 13, 2014 at 6:26 PM, Alexander Björling <
> alex.bjorling at gmail.com> wrote:
>
>>
>> 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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>
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