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

[Eugene Valkov]

Hi Elaine,

Thanks for a quick response and for clarifying this a bit. However, I am
still none the wiser as to why there is a discrepancy between the SAXS fits
reported by the version Chimera uses and the FoxS from the IMP suite or the
Sali lab webserver. For the record, I think Chimera reports the more
accurate values as they are in rough agreement with those from another
program, Crysol.

Regards,
Eugene

On 3 August 2015 at 19:16, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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