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 | fergal.duffy@cidresearch.org