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

IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint()

is indeed a sigmoidal function modulated by two parameters sigma (inflection) and psi (baselines).

The maximal length of the crosslinker is passed through "length=..." in the constructor.

There is a linear part, but that is just a soft bias to avoid particles getting dispersed, since the potential is flat

at high distance values. The slope of the linear part is 0.01-0.02 Score Unit/ Angstrom, can be changed using "slope=..."

Riccardo Pellarin, PhD

===================

Institut Pasteur

CNRS UMR 3528

25, rue du Docteur Roux
75724 Paris Cedex 15, France

+33 (0)1 44 38 93 63

On Fri, Jun 9, 2017 at 1:41 AM, 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.

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.

Regards,

Fergal

Fergal Duffy
Postdoctoral Researcher

Center for Infectious Disease Research
307 Westlake Ave N, Suite 500 | Seattle, WA 98109
206.256.7435 | ">

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