Re: [IMP-users] PMI crosslinks and state ambiguity

> 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

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+33 (0)1 44 38 93 63

On Tue, Feb 23, 2021 at 2:30 PM Andrea Graziadei <">> 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
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