<div dir="ltr"><div><div><div>Hello,<br><br></div>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<br>
<br>/*<br> * compute the square modulus of the structure factor, averaging on the surface<br> * kx*kx + ky*ky + kz*kz = krr*krr<br> * note that this is correct only for a (on the macroscopic scale)<br> * isotropic system.<br>
*/<br></div><br>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.<br>
<br>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. <br><br>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.<br>
<br></div>Thanks for your time and help<br><br>Best regards<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Aug 7, 2014 at 9:44 PM, Alexey Shvetsov <span dir="ltr"><<a href="mailto:alexxy@omrb.pnpi.spb.ru" target="_blank">alexxy@omrb.pnpi.spb.ru</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi!<br>
<br>
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<br>
<br>
<br>
[1] <a href="https://www.researchgate.net/publication/260218253_Structure_of_RecX_protein_complex_with_the_presynaptic_RecA_filament_molecular_dynamics_simulations_and_small_angle_neutron_scattering" target="_blank">https://www.researchgate.net/<u></u>publication/260218253_<u></u>Structure_of_RecX_protein_<u></u>complex_with_the_presynaptic_<u></u>RecA_filament_molecular_<u></u>dynamics_simulations_and_<u></u>small_angle_neutron_scattering</a><br>
<br>
[2] <a href="https://gerrit.gromacs.org/#/c/2659/" target="_blank">https://gerrit.gromacs.org/#/<u></u>c/2659/</a><br>
<br>
Anjaiah Nalaparaju писал 06-08-2014 08:11:<div class="HOEnZb"><div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs Developers,<br>
<br>
I have just started looking into the option for calculating SAXS<br>
profile for a protein using gromacs. I found in sfactor.c , for<br>
calculating the structure factor spherical averaging in not<br>
implemented. Where as in nsfactor.c, I guess it is implemented. Could<br>
you please let me know the reason for implementing different approach<br>
for SAXS and SANS calculation. I think in SAXS calculation also<br>
spherical averaging might be needed to match the calculated profile<br>
with experiments. If not spherical averaged I found orientation of<br>
protein has effect on the profile. Any clarification on this query is<br>
greatly appreciated.<br>
<br>
Thanks in Advance.<br>
Best regards<br>
</blockquote>
<br></div></div><span class="HOEnZb"><font color="#888888">
-- <br>
Best Regards,<br>
Alexey 'Alexxy' Shvetsov, PhD<br>
Department of Molecular and Radiation Biophysics<br>
FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,<br>
Leningrad region, Gatchina, Russia<br>
mailto:<a href="mailto:alexxyum@gmail.com" target="_blank">alexxyum@gmail.com</a><br>
mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru" target="_blank">alexxy@omrb.pnpi.spb.ru</a><br>
-- <br>
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