[Chimera-users] FoxS in Chimera for SAXS curve fitting
eugene.valkov at gmail.com
Wed Aug 5 00:20:31 PDT 2015
Thanks Ben. If the newer FoxS versions have more robust algorithms to deal
with overfitting then I would heartily recommend that Chimera developers
would redirect to the Sali server, which runs up-to-date software. There is
an option of launching FoxS locally so I guess there is no reason not to
use the most up-to-date version, but this does require some effort on the
part of the user to install the IMP suite and point to the executable.
Notwithstanding, I think the ability to fit the SAXS curve directly from a
model loaded in Chimera and produce a very nice publication-quality graph
is super-helpful and easy.
On 5 August 2015 at 02:20, Ben Webb <ben at salilab.org> wrote:
> On 08/03/2015 10:51 AM, Eugene Valkov wrote:
>> 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.
> Dina would be the person to ask (since she wrote FoXS). Her contact
> details are on the FoXS website.
> Chimera folks: I'm not sure why the version of FoXS you're using is so old
> (if it's really IMP 2.1, that was released in 2013). If possible, Chimera
> should just talk directly to the Sali lab FoXS webserver. If that's not
> practical, it should be straightforward to update your web service to use
> the latest IMP 2.5.0 release.
> For the record, I think Chimera reports
>> the more accurate values as they are in rough agreement with those from
>> another program, Crysol.
> It's far more likely that you're seeing overfitting here. That was
> certainly an issue in older versions of FoXS, long since fixed at our end.
> ben at salilab.org http://salilab.org/~ben/
> "It is a capital mistake to theorize before one has data."
> - Sir Arthur Conan Doyle
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