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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 Center for Infectious Disease Research |