The example in the manual deals only with the commandline FoXS tool. I did mange to find some examples although they were very well hidden (in the sense that my goggle keywords "IMP python modelling SAXS example" and similar did not return anything useful). But clicking the reference guide and going to class examples https://integrativemodeling.org/2.5.0/doc/ref/class_example_index.html produced a wealth of useful scripts to learn from!:)
I also learned that one can use https://integrativemodeling.org/2.5.0/doc/ref/namespaceIMP_1_1modeller.html the IMP saxs restraints in Modeller or the Modeller homology restraints in IMP. I'll first try to use the IMP SAXS restraints in modeller together with some CG optimization just to polish the model (the alignment with SAXS is already quite good).
@Edelmiro Thanks for the interesting idea, but I'll try to do this with as few tools as possible:)
Thanks and all the best, Ajasja
On 30 October 2015 at 10:43, Edelmiro Moman moman@prosciens.com wrote:
> Yet another option would be converting your SAXS envelope to an (pseudo) > electron density map, (rigid) docking your model into the map with > something like SITUS and then refining your model to fit the (pseudo) > electron density with something like NMFF. > > I have done it in the past with good results (it is very straightforward > and you obtain a very nice trajectory/movie of the NM fitting). > > > On 30/10/15 09:59, modeller_usage-request@salilab.org wrote: > >> [modeller_usage] Modelling with SAXS data >> > > > -- > Edelmiro Moman, PhD > ProSciens, computer-aided drug design > Caminho Bastida, 162 > E-15405 Ferrol > Galicia, Spain > > Phone : +352 621-511-423 > E-mail : moman@prosciens.com > http://prosciens.com >