[gmx-developers] Debye formula (spherical averaging) in SAXS calculation !

[Alexey Shvetsov]

Hi!

Well g_sans was written by me to compare MD simulations with our 
experimental SANS data (see for example [1]), while g_saxs was splited 
of g_rdf. However there is unmerged patch containing waxs utility with 
Debye averaging [2]. So its somehow historical reasons why there no 
spherical avareging in g_saxs


[1] 
https://www.researchgate.net/publication/260218253_Structure_of_RecX_protein_complex_with_the_presynaptic_RecA_filament_molecular_dynamics_simulations_and_small_angle_neutron_scattering

[2] https://gerrit.gromacs.org/#/c/2659/

Anjaiah Nalaparaju писал 06-08-2014 08:11:
> Dear Gromacs Developers,
> 
> I have just started looking into the option for calculating SAXS
> profile for a protein using gromacs. I found in sfactor.c , for
> calculating the structure factor spherical averaging in not
> implemented. Where as in nsfactor.c, I guess it is implemented. Could
> you please let me know the reason for implementing different approach
> for SAXS and SANS calculation. I think in SAXS calculation also
> spherical averaging might be needed to match the calculated profile
> with experiments. If not spherical averaged I found orientation of
> protein has effect on the profile. Any clarification on this query is
> greatly appreciated.
> 
> Thanks in Advance.
> Best regards

-- 
Best Regards,
Alexey 'Alexxy' Shvetsov, PhD
Department of Molecular and Radiation Biophysics
FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
Leningrad region, Gatchina, Russia
mailto:alexxyum at gmail.com
mailto:alexxy at omrb.pnpi.spb.ru