First of all I would just like to say that I'm a very happy modeller user and that things have been running pretty smoothly:)
We have obtained recently some SAXS data for a specific protein (that we hope is a monomer in solution). I have already built several models of this protein, but now I would like to refine it using SAXS data.
As far as I know I have three options:
- Use the SAXS modeller class https://salilab.org/modeller/manual/node426.html and hope for the best (I found an old thread https://salilab.org/archives/modeller_usage/2011/msg00330.html stating that it's no longer supported). - Use FoXS to screen models after I have generated them using modeller - Switch to IMP (I could only find one example http://integrativemodeling.org/keystone2015/IMP_SAXS.pdf of the IMP python interface) and add the restraints in IMP.
Any comments and suggestions are welcome. in particular I'd like to know: how/if restraints be added in modeller based on SAXS data? And if it really is a very bad idea to use this unsupported functionality?
Thank you & best regards, Ajasja Ljubetič, National Institute of Chemistry, Slovenia
On 10/29/15 8:10 AM, Ajasja Ljubetič wrote: > Any comments and suggestions are welcome. in particular I'd like to > know: how/if restraints be added in modeller based on SAXS data? And if > it really is a very bad idea to use this unsupported functionality?
All of our recent SAXS work is in IMP, not Modeller, so it's not a great idea to use the Modeller code. If you want to build models then filter against SAXS data, FoXS is definitely the way to go. You can certainly include SAXS as a restraint during modeling, but it's expensive to evaluate.
The slides you referenced pull in various parts of the IMP documentation. For example, the section on FoXS is largely based on the example in the IMP manual: http://integrativemodeling.org/2.5.0/doc/manual/foxs_nup133.html
Ben Webb, Modeller Caretaker