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

Anjaiah Nalaparaju anjai.che at gmail.com
Fri Aug 8 10:15:49 CEST 2014


I just want to check, in the saxs module from the latest gromacs version
there is a loop in sfactor.c under function " extern void
compute_structure_factor " as mentioned below

 *  compute the square modulus of the structure factor, averaging on the
 *  kx*kx + ky*ky + kz*kz = krr*krr
 *  note that this is correct only for a (on the macroscopic scale)
 *  isotropic system.

1. Does it corresponds to kind of spherical averaging by rotating
scattering wave vector "q" over the surface. If not, what is the reason to
have this loop. I think, we just need to calculate structure factor one
time for a given scattering angle. So I am not sure why this loop is used.

2.  If it is one way of implementing spherical averaging, is it accurate to
do like this.Because, I found there is some change in the SAXS profile if I
change the orientation of protein and calcualte saxs.

3. How can we use the saxs module in latest gromacs version to get the
agreement between calculated and experimental data and also to remove the
orientation effect. I mean to get result close to the debye implementation
with the present version.

Thanks for your time and help

Best regards

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

> 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
> --
> Gromacs Developers mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-developers_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> or send a mail to gmx-developers-request at gromacs.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20140808/2d3ea196/attachment.html>

More information about the gromacs.org_gmx-developers mailing list