FoxS in Chimera for SAXS curve fitting
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
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@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
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@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@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
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@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@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@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
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 -- ben@salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
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. Regards, Eugene On 5 August 2015 at 02:20, Ben Webb <ben@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 -- ben@salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
participants (3)
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Ben Webb -
Elaine Meng -
Eugene Valkov