[Chimera-users] FoxS in Chimera for SAXS curve fitting

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 3 10:16:27 PDT 2015


Hi Eugene,
When you run FoXS from Chimera (Tools.. Higher-Order Structure… Small-Angle X-Ray Profile) some user-settable options are shown in the dialog if you click the Options button.  Other than those settings, some information about the web service is shown in the Reply Log (in menu under Favorites):

Web Service: SAXS2.1 uses the FoXS program (D. Schneidman-Duhovny, M. Hammel, JA. Tainer, and A. Sali. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophysical Journal 2013. 105 (4), 962-974) to calculate a theoretical small-angle X-ray scattering profile from a structure and optionally compare it to an input experimental profile.
Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/SAXS2Service

I don’t know if “2.1” is enough version information.  You can see from the URL that it uses the service provided by our lab, the RBVI.  If by “online server” you mean the one at the Sali Lab website ( <http://modbase.compbio.ucsf.edu/foxs/> ), that is a separately controlled service.  I don’t know if they are running a different version, but comparing the Chimera dialog to the options on the site, the default settings appear to be the same.  Some are greyed out in the Chimera dialog if you don’t specify an experimental profile because otherwise, they do not apply.  I don’t see any mention of version at the Sali Lab site, and I don’t know if your binary is marked with a version number.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 3, 2015, at 1:58 AM, Eugene Valkov <eugene.valkov at gmail.com> wrote:
> 
> I was wondering what version of FoxS the current release of Chimera employs for goodness-of-fit calculations to small-angle X-ray scattering curves using crystal structure models? Also, if any specific parameters are used other than what is default?
> 
> I obtain quite different values using standalone FoxS binary or using the online server versus what is output by Chimera.
> 
> Thanks,
> Eugene




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