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

[Anjaiah Nalaparaju]

Thanks very much for providing the details. It is very nice contribution
you have made to the package and hope to see the new module merged gromacs
version soon.

Best regards


On Thu, Aug 7, 2014 at 9:44 PM, Alexey Shvetsov <alexxy at omrb.pnpi.spb.ru>
wrote:

> 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
> --
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