Hello,
I am building a system using topolgyReader in PMI in imp-2.13. I have built a 2-state system by
bm = IMP.pmi.macros.BuildSystem(m, force_create_gmm_files=False) bm.add_state(topology) bm.add_state(topology2)
I then add crosslinks to the system with IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
How does the system handle the state ambiguity? If a crosslink is satisfied at a particular frame only in state1, it should count overall as satisfied (given crosslinks are measured on in solution ensembles), also when for example analysing %ge violations with imp-sampcon or similar modules... >From what I understand, It looks to me like this is handled correctly in the sampling, but imp-sampcon and pmi_analysis are not yet equipped to deal with this (slicing on %ge over length does not report crosslinks as satisfied if they are under maximum distance in one of the states only). Is this correct?
Many thanks,
Andrea