Re: [IMP-users] Issue with using SAXS Restraint in IMP

[Ben Webb <>]

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
--
                      https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle