Re: [IMP-users] Sigmoidal crosslinks in IMP.pmi 2.7.0

[Ben Webb <>]

On 6/8/17 4:41 PM, Fergal Duffy wrote:
> I am using IMP.pmi to model a protein complex using MS crosslinks. I 
> notice that the IMP.pmi crosslinking function, 
> IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint(), 
> scores crosslinks basically as a linear function of crosslink distance. 
> The crosslink length is basically irrelevant here, shorter=better.

I don't think that's right, although Riccardo would know for sure. The 
restraint *does* include a linear term, but my understanding is that's 
intended to gradually pull in residue pairs that far exceed the 
crosslink length. At shorter distances the scoring is Bayesian, and 
certainly does use the crosslink length.

> Ideally, I would like to score crosslinks as a sigmoid function, with 
> crosslinks inside the specified ‘length’ dropping in score. I notice 
> that there is a deprecated SigmoidCrossLinkMS() function in IMP, which 
> uses an IMP.pmi.SigmoidRestraintSphere to model the crosslinks. Is there 
> a reason this is deprecated? Should I be using it? It seems to offer 
> functionality not available elsewhere.

It's deprecated because the current Bayesian formalism is superior, but 
there are some older published works that used that restraint (and we 
want them to still be reproducible). It's probably not a good idea to 
use it in modern applications.

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