> 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),

Yes, precisely.

> 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).

I think that most of the standard analysis tools are not adapted to deal with multistate sampling.

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 Tue, Feb 23, 2021 at 2:30 PM Andrea Graziadei graziadei.a@gmail.com wrote:

> 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 > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >