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

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 3 11:03:09 PDT 2015


Sorry, I’m afraid I’m in the same boat.  We would need version numbers (or build dates) for all three things to know for sure: your local binary, the web service at the Sali Lab website, and the web service at the RBVI.  We aim to report all we know about the software version run by RBVI webservices in the Reply Log.
Elaine


> On Aug 3, 2015, at 10:51 AM, Eugene Valkov <eugene.valkov at gmail.com> wrote:
> 
> 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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