On 8/26/20 2:43 PM, Sumner, Jacob wrote: > I have been using IMP for the past two weeks or so, and I would like to > restrain the modeling I am doing with pmi using SAXS data. However, I > have not been able to find the location of the SAXS restraint
IMP.pmi.restraints.saxs.SAXSRestraint is the one you probably want to use with PMI. See the actin tutorial for an example: https://integrativemodeling.org/tutorials/actin/modeling.html
> it seems the one that was located in pmi.restraints was deprecated.
What makes you think that? If a class in IMP is deprecated, it should explicitly say so (and we should fix it if it's saying something misleading).
> When I try to access the IMP.saxs package, it seems that doesn't exist > either.
Not sure what you mean here. You get an ImportError?
(It's possible but rather unlikely that your copy of IMP was built without IMP.saxs; certainly none of the binary packages we produce are built that way. If IMP.saxs didn't exist you wouldn't be able to even import IMP.pmi.restraints.saxs anyway, since it in turn imports IMP.saxs.)
> When I try to run pmi.restraints.saxs.SAXSRestraint, it says I > need to install isd2
It used to say "Module isd2 not installed. Cannot use SAXSISDRestraint". This is perhaps a bit misleading because SAXSRestraint works just fine; you only need to install isd2 if you want to use SAXSISDRestraint, which is experimental and not really intended for general use yet. I actually removed that print a couple of weeks ago: https://github.com/salilab/pmi/commit/8fac143b3
Ben