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 riccardo.pellarin@pasteur.fr +33 (0)1 44 38 93 63
On Fri, Jun 9, 2017 at 1:41 AM, Fergal Duffy fergal.duffy@cidresearch.org 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 http://www.cidresearch.org/ > 307 Westlake Ave N, Suite 500 | Seattle, WA 98109 > 206.256.7435 <%28206%29%20256-7435> | *fergal.duffy@cidresearch.org > fergal.duffy@cidresearch.org* > > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > >